Compositions and methods for rapid identification and phenotypic antimicrobial susceptibility testing of bacteria and fungi

ABSTRACT

The present invention relates to compositions and methods for the use of polymerase chain reaction (PCR) as a reporter assay for rapid and simultaneous bacterial identification and phenotype testing for antimicrobial susceptibility (AST). The current invention uses a strategy that has shown the ability for multiplexing and for handling polymicrobial samples for antimicrobial susceptibility testing.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.16/950,160 filed on Nov. 17, 2020, which claims the benefit of priorityto U.S. Provisional Application No. 62/938,144 filed on Nov. 20, 2019,which are both hereby incorporated in their entireties by reference.

FIELD OF THE INVENTION

The present disclosure relates to the field of molecular diagnostics,and more particularly to the identification and the determination ofantimicrobial susceptibility of bacteria from biological samples.

BACKGROUND OF THE INVENTION

There is an urgent need for the development or rapid and convenientmethods for the detection, identification and determination ofantimicrobial susceptibility of bacterial pathogens in clinical samplesto guide the diagnosis and treatment of infectious disease. A goodexample for this need is in bloodstream infections (BSI). BSI ranksamong the top seven causes of death in North America and Europe with anestimated 1.7 million sepsis events/year in the US contributing to270,000 deaths/year and $14 billion annual US healthcare costs. Adecreased time to directed antimicrobial therapy has been shown toimprove morbidity and mortality in septic patients, which then resultsin decreased length of stay (LOS) and lower hospital costs. Fastersusceptibility results will also enable more rapid antimicrobialde-escalation leading to less adverse effects and decreased contributionto drug resistance. Therefore, there remains a need for the developmentof an assay and testing system that will provide rapid phenotypicantimicrobial susceptibility results in BSIs enabling clinicians toprovide the most appropriate antimicrobial therapies more quicklyleading to improved patient outcomes.

Polymicrobial bloodstream infection (BSI), defined as the presence of atleast two different microorganisms found from the blood cultures, hasbeen reported increasingly, with rates ranging from 6% to 32% of all BSIepisodes. The mortality rate of hospitalized patients with polymicrobialBSIs ranged from 21% to 63%, approximately twice the rate of those withmonomicrobial infections.

Traditional Antimicrobial Susceptibility Testing (AST) is performed bygrowing a given bacteria in the presence of a given antimicrobial—thiscan be done in both liquid culture and on solid agar media. The two mostcommon methods of AST are: 1) Microbroth Dilution, and 2) Disk Diffusion(aka Kirby-Bauer). The microbroth dilution method provides bothquantitative (Minimum Inhibitory Concentration) and qualitative(Susceptible, Intermediate, and Resistant) results. The disk diffusionmethod provides only qualitative results.

Microbroth dilution is performed by incubating a given bacteria in thepresence of multiple concentrations of antimicrobial. Followingincubation, growth/no growth of the bacteria is observed at eachconcentration of antimicrobial. The lowest concentration at which nogrowth is observed is the Minimum Inhibitory Concentration (MIC), andhas units of ug/mL. Established guidelines provide the “breakpoint”where experimentally determined MIC values for specific bacterial groupsor species are interpreted as susceptible, intermediate, or resistant(SIR) to the given antimicrobial.

Disk diffusion is performed by creating a “bacterial lawn” of a givenbacteria on solid agar media, and then placing a singular antibioticdisk onto the agar media. The antibiotic in the disk diffuses into themedia, and following incubation, a circular zone of inhibition aroundthe disk is created. The diameter of the zone along with information onthe bacterial species and antimicrobial is used in conjunction withreference established diameter breakpoints to determine whether thepathogen is susceptible, intermediate, or resistant to the givenantimicrobial.

In general, the two most commonly used guidelines for interpreting ASTresults are guidelines from the: 1) Clinical Laboratory StandardsInstitute (CLSI), and 2) European Committee on AntimicrobialSusceptibility Testing (EUCAST). The US uses the CLSI guidelines whilethe European countries use the EUCAST guidelines. The current versionfrom CLSI is M100 ED30, while the current version from EUCAST is Version10.

SUMMARY OF THE INVENTION

The present invention relates to a polymerase chain reaction (PCR)-basedrapid identification and antimicrobial susceptibility testing (ID/AST)System that supports an automated workflow for specific assay panelsutilizing PCR technology for the rapid and simultaneous identificationand determination of antimicrobial susceptibility of bacteria, directlyfrom biological samples, e.g. from positive blood cultures for use inclinical laboratories. This system also has the capability of utilizingand analyzing samples from other sample types such as urine andrespiratory infections. The PCR-based rapid ID/AST System uses thefunctionalities of instrumentation, consumables, reagents, and datamanagement to provide a workflow from sample processing with reagents toresult interpretation. By performing a single PCR assay, targetidentification and antimicrobial susceptibility results are outputs fromthe system.

The present invention also relates to a PCR-based rapid ID/ASTbloodstream infection (BSI) panel that is an in vitro diagnostic testutilizing PCR Technology for the rapid identification of select bacteriaor fungi and performing phenotypic antimicrobial susceptibility testing(AST) on the PCR-based rapid ID/AST system. The PCR-based rapid ID/ASTBSI assay can be performed directly on positive blood culture samples,on pre-positive blood cultures, or potentially directly from patientserum. This assay is indicated as an aid in diagnosing and identifyingantimicrobial susceptibility of specific pathogens that can causebacteremia. This panel is designed to analyze the most common BSIGram-negative and Gram-positive pathogens, with the potential for Fungi.The TaqMan 5′nuclease real-time PCR assay configuration coupled with theID strategy should provide the capability to provide Minimum InhibitoryConcentration (MIC) and Susceptible, Intermediate and Resistant (SIR)information for polymicrobial samples, monomicrobial samples, andisolate testing as needed. These results should be used in conjunctionwith other clinical and laboratory findings. Standard laboratoryprotocols for processing positive blood cultures should be followed toensure availability of isolates for supplemental testing as needed.

The present invention also relates to PCR-based rapid ID/AST phenotypicscreening tests that are in vitro diagnostic tests utilizing PCRTechnology for the rapid identification and phenotypic susceptibilitytesting of a target pathogen or group of pathogens for a single drug,class of drugs, or combination of drugs. The PCR-based rapid ID/ASTscreening assays are performed either directly from clinical samples orfrom bacterial/fungal isolates. These assays will indicate the presenceof problematic drug resistant pathogens to aid in patient and hospitalsafety. Examples of these types of tests are for Methicillin-ResistantStaphylococcus aureus (MRSA), Vancomycin-Resistant Staphylococcus aureus(VRSA), Vancomycin-resistant Enterococci (VRE), Carbapenem-ResistantEnterobacteriaceae (CRE), Candida auris, and MDR Neisseria gonorrhoeae.

Therefore, one aspect of the present invention relates to a method ofperforming a single quantitative real-time PCR assay as a reporter inthe presence of at least one concentration of at least one antimicrobialor antimicrobial class to simultaneously identify and determine theantimicrobial susceptibility of a group of bacteria or fungi that havesimilar or identical clinical breakpoints for at least one antimicrobialor one antimicrobial class. In one embodiment, the target group ofbacteria or fungi are present in bloodstream infections (BSI,gastrointestinal infections or colonization, respiratory infections orcolonization, urinary infections or colonization, nasal infections orcolonization, rectal infections or colonization, or wound infections. Inone embodiment, identification of the group of bacteria or fungi is bydetecting a signal that is specific to the group of bacteria or fungi.In one embodiment, the specific signal is detected by using primer andprobe oligonucleotides that hybridize more selectively to a target genethat is from the group of bacteria or fungi than to the target gene thatis not from the group of bacteria or fungi. In one embodiment, thetarget gene is selected from rplP, ompA, tuf, rpoB, ddl, ddlA, fdnGsodA, gyrB, O-antigen acetylase, ecfX, tusA, CPE, sip, and nuc.

In another embodiment, the group of bacteria or fungi represents ataxonomic Order. In one embodiment, the taxonomic Order is the OrderEnterobacterales. In another embodiment, the group of bacteria or fungicomprises a taxonomic Family. In one embodiment, the taxonomic Family isselected from Enterobacteriaceae, Yersiniaceae, Morganellaceae, or acombination of said families. In yet another embodiment, the group ofbacteria or fungi comprises a taxonomic Genus. In one embodiment, thetaxonomic Genus is selected from Enterococcus, Candida, Pseudomonas,Acinetobacter, Staphylococcus, Stenotrophomonas, Streptococcus, andEscherichia, Klebsiella, Enterobacter, Salmonella, Citrobacter,Serratia, Shigella, Corynebacterium, Micrococcus, Bacillus, Haemophilus,Propionibacterium, Bacteroides, Clostridium, Peptostreptococcus,Fusobacterium, Pasteurella, Lactobacillus, Aerococcus, Prevotella,Burkholderia, Moraxella, Vibrio, Listeria, Plesiomonas, Yersinia,Morganella, Providencia, or Proteus.

In another embodiment, the group of bacteria or fungi represents ataxonomic Species. In one embodiment, the taxonomic Species is selectedfrom Enterococcus faecalis (Efs), Enterococcus faecium (Efm),Escherichia coli (Eco), Klebsiella pneumoniae (Kpn), Klebsiella oxytoca(Kox), Enterobacter cloacae (Ecl), Enterobacter aerogenes (Kae),Citrobacter freundii (Cfi), Citrobacter koseri (Cko), Morganellamorganii (Mmg), Providencia stuartii (Pst), Proteus mirabilis (Pms),Proteus vulgaris (Pvs), Candida albicans (Cal), Candida auris (Cau),Pseudomonas aeruginosa (Pae), Acinetobacter baumannii (Abi),Acinetobacter pittii (Api), Acinetobacter nosocomialis (Ano),Haemophilus influenza, Listeria monocytogenes, Staphylococcus aureus(Sau), Staphylococcus lugdunensis, Staphylococcus epidermidis (Sep),Stenotrophomonas maltophilia (Sma), Streptococcus pneumoniae (Spn),Streptococcus agalactiae (Sag), Streptococcus pyogenes (Spy),Plesiomonas shigelloides, Vibrio parahaemolyticus, Vibrio vulnificus, orVibrio cholerae.

In yet another embodiment, the method further comprises a step selectedfrom verifying the identification of the group of bacteria or fungi withadditional primer and probe oligonucleotides that hybridize moreselectively to a second target gene that is from the group of targetbacteria or fungi than to the second target gene that is not from thegroup of bacteria or fungi or determining a mechanism for anantimicrobial susceptibility phenotype or for a toxin or virulencephenotype, or both verifying and determining steps. In anotherembodiment, the method further comprises simultaneously identifying anddetermining the antimicrobial susceptibility of more than one groups ofbacteria or fungi wherein each group of bacteria or fungi has similar oridentical clinical breakpoints for at least one antimicrobial or oneantimicrobial classes.

In another aspect, the present invention relates to a method ofperforming a single quantitative real-time PCR assay as a reporter inthe presence of at least one concentration of at least one antimicrobialor antimicrobial class to simultaneously identify and determine theantimicrobial susceptibility of bacteria of the Enterobacterales Orderto an antimicrobial or a class of antimicrobials by using primer andprobe oligonucleotides that hybridize more selectively to a target genethat is in the Enterobacterales taxonomic Order than to the target genethat is not in the Enterobacterales taxonomic Order. In one embodiment,the target gene is selected from rplP, gyrB, and rpoB. In oneembodiment, the primer and probe oligonucleotides that hybridize moreselectively to the target gene that is in the Enterobacterales taxonomicOrder than to the target gene that is not in the Enterobacteralestaxonomic Order comprise the nucleotide sequences comprising SEQ ID NOs:1-16. In one embodiment, the primer and probe oligonucleotides thathybridize more selectively to gyrB in the Enterobacterales Order than togyrB in the non-Enterobacterales Order comprise the nucleotide sequencescomprising SEQ ID NOs: 8-10.

In another aspect, the present invention relates to a method ofperforming a single multiplexed quantitative real-time PCR assay as areporter in the presence of at least one concentration of at least oneantimicrobial or antimicrobial class to simultaneously identify anddetermine the antimicrobial susceptibility of a plurality of bacterialor fungal strains from a biological sample, i.e. from a polymicrobialbiological sample. In one embodiment, the biological sample is selectedfrom whole blood, plasma, serum, red blood cell fraction, saliva,cerebrospinal fluid, semen, stool, urine, nasal swab, wound swab, dermalswab, rectal swab, bile, lymph, sputum, lavage fluid, or a combinationthereof. In one embodiment, the biological sample is whole blood,plasma, serum or a combination thereof. In one embodiment, thebiological sample is cultured prior to performing the PCR assay. Inanother embodiment, the biological sample is a bacterial or fungalisolate. In another embodiment, the plurality of bacterial or fungalstrains are grouped into at least one group of bacteria or fungi thathave similar or identical clinical breakpoints for at least oneantimicrobial or antimicrobial class. In one embodiment, the pluralityof bacterial or fungal strains are grouped into more than one groups ofbacteria or fungi wherein each group of bacteria or fungi has similar oridentical clinical breakpoints for at least one antimicrobial or oneantimicrobial class.

In another embodiment, the identification of the plurality of bacterialstrains utilizes a plurality of strain-specific 5′ nuclease (TaqMan)oligonucleotide probes, each labeled with fluorescent dyes that havedifferent emission wavelengths. In one embodiment, one or more of theplurality of strain-specific 5′ nuclease (TaqMan) oligonucleotide probescomprises probes that utilize the Temperature Assisted Generation ofSignal (TAGS) technology. In another embodiment, the method furthercomprises a step selected from verifying the identification of theplurality of bacterial or fungal strains, or determining a mechanism foran antimicrobial susceptibility phenotype or for a toxin or virulencephenotype, or both verifying and determining steps.

In another aspect, the present invention relates to a method comprisingperforming a single quantitative real-time PCR assay in the presence ofat least one concentration of at least one antimicrobial or class ofantimicrobials to simultaneously identify and determine Susceptible,Intermediate and Resistant (SIR) information for a target bacterial orfungal strain or for a target group of bacteria or fungi to theantimicrobial or the class of antimicrobials wherein the identificationof the target strain or target group and the determination of SIRinformation are derived from one or more mathematical relationshipsassociated with PCR data. In one embodiment, the mathematicalrelationship is selected from Threshold Cycle (Ct), Slope, Inflection ofa sigmoid curve fit, Absolute Fluorescence Intensity (AFI), or EndpointRelative Intensity (ERI). In another embodiment, the mathematicalrelationship is a relative expression between different antimicrobialconcentrations or different antimicrobials and is selected from □Ct,2{circumflex over ( )}(□Ct), □Inflection□□□AFI, or □ERI. In oneembodiment, the mathematical relationship is a combination ofmathematical relationships selected from Threshold Cycle (Ct), Slope,Inflection of a sigmoid curve fit, Absolute Fluorescence Intensity(AFI), or Endpoint Relative Intensity (ERI). In yet another embodiment,the mathematical relationship is a combination of relative expressionsbetween different antimicrobial concentrations or differentantimicrobials and is selected from □Ct, 2{circumflex over ( )}(□Ct),□Inflection□□□AFI, or □ERI. In another embodiment, the method furthercomprises a step of selected from verifying the identification of thetarget bacterial or fungal strains or target group of bacteria or fungi,or determining a mechanism for an antimicrobial susceptibility phenotypeor for a toxin or virulence phenotype, or both verifying and determiningsteps. In another embodiment, the method further comprises identifyingand determining the antimicrobial susceptibility of more than one targetbacteria or fungi strains or more than one target groups of bacteria orfungi wherein each target strain or target group has similar oridentical clinical breakpoints for at least one antimicrobial or oneantimicrobial class.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. In the absence of antimicrobial (shown as Reference), bacteriahave ongoing genomic DNA replication. In the presence of anantimicrobial, resistant bacteria will replicate with similar number ofgenome copies as the Reference, while susceptible bacteria willexperience inhibition of replication resulting in fewer copies. Thisdifference in growth provides a phenotypic readout that can bedetermined by qPCR.

FIG. 2. A The raw qPCR data is depicted as growth curves wherefluorescence (e.g. from a TaqMan probe) is measured at each PCR cycle.For the resistant isolate, the growth curve appears similar irrespectiveof incubation for four hours at different antimicrobial concentrations,whereas in the susceptible isolate, a dose-dependent decrease influorescent intensity and increase in the number of cycles required forthe signal to cross background (threshold) level, which is commonlyreferred as the Cycle threshold or Ct value. B The same qPCR data isrepresented based on the Ct value, where a resistant isolate has littleor no change in Ct value as a function of antimicrobial concentration,while a susceptible isolate has a dose dependent increase in Ct value bydetecting a smaller number of replicating bacteria.

FIG. 3. A Mathematical relationships such as “Slope”, “Ct”,“Inflection”, “Absolute Fluorescence Intensity (AFI)”, and “EndpointRelative Intensity (ERI)” describe the behavior of the raw qPCRamplification curve. B These features can further be evaluated as afunction of antimicrobial exposure by relating numerical values obtainedin the presence of antimicrobial back to the numerical values obtainedin the absence of the antimicrobial. Relative changes in these features,such as “□Ct”, “□Inflection” or “□AFI” can then be used to determinestrain MIC to a given drug allowing strain resistance and susceptibilitydetermination utilizing approved breakpoints.

FIG. 4. Partitioning models were used to classify bacteria isolates asresistant or susceptible. Partitioning utilizes the Gini Index todetermine which feature and threshold maximizes dispersion of the twoclasses. Only two splits are utilized to prevent overfitting and allowsfor graphical representation in two dimensions for easy visualization.

FIG. 5. PCR assays using primers and probe disclosed in TABLE III thattarget the gyrB gene were tested against common Gram-negative pathogens.Growth curves are observed only for the species that constitute theorder Enterobacterales (including E. coli, K. pneumoniae, E. cloacae, K.oxytoca, K. aerogenes, S. marcescens, and P. mirabilis). No meaningfulamplification was observed for non-target organisms.

FIG. 6. PCR assays using primers and probe disclosed in TABLE II thattarget the rplP gene were tested against common Gram-negative pathogens.Growth curves are observed only for the species that constitute theorder Enterobacterales. No meaningful amplification was observed fornon-target organisms.

FIG. 7. PCR assays using primers and probe disclosed in TABLE IV thattarget the rpoB gene were tested against common Gram-negative pathogens.Growth curves were observed only for the species that constitute theorder Enterobacterales. No meaningful amplification was observed fornon-target organisms.

FIG. 8. PCR assays using primers and probe disclosed in TABLE V thattarget the ompA gene were tested against common Gram-negative pathogens:E. coli, K pneumoniae, E. cloacae, K. oxytoca, K aerogenes, S.marcescens, P. mirabilis, S. maltophilia, P. aeruginosa, A. baumannii,and A. pittii. Growth curves are observed only for the prevalentpathogens that are within the genus Acinetobacter (A. baumannii and A.pittii). No meaningful amplification was observed for non-targetorganisms.

FIG. 9. PCR assays using primers and probe disclosed in TABLE VI thattarget the rpoB gene were tested against common Gram-negative pathogens.Growth curves are observed only for the prevalent pathogens that arewithin the genus Acinetobacter. No meaningful amplification was observedfor non-target organisms.

FIG. 10. PCR assays using primers and probe disclosed in TABLE VII thattarget the gyrB gene were tested against common Gram-negative pathogens.Growth curves are observed only for the prevalent pathogens that arewithin the genus Acinetobacter. No meaningful amplification was observedfor non-target organisms.

FIG. 11. PCR assays using primers and probe disclosed in TABLE VIII thattarget the tuf gene were tested against common Gram-negative pathogens:E. coli, K pneumoniae, E. cloacae, K. oxytoca, K aerogenes, S.marcescens, P. mirabilis, S. maltophilia, P. aeruginosa, A. baumannii,and A. pittii. Growth curve is observed only for pathogens within thegenus Pseudomonas (P. aeruginosa). No meaningful amplification wasobserved for non-target organisms.

FIG. 12. PCR assays using primers and probe disclosed in TABLE IX thattarget the gyrB gene were tested against common Gram-negative pathogens.Growth curve is observed only for pathogens within the genus Pseudomonas(P. aeruginosa). No meaningful amplification was observed for non-targetorganisms.

FIG. 13. PCR assays using primers and probe disclosed in TABLE X thattarget the rpoB gene were tested against common Gram-negative pathogens.Growth curve is observed only for pathogens within the genus Pseudomonas(P. aeruginosa). No meaningful amplification was observed for non-targetorganisms.

FIG. 14. PCR assays using primers and probe disclosed in TABLE XI thattarget the fdnG gene were tested against common Gram-negative pathogens:E. coli, K. pneumoniae, E. cloacae, K. oxytoca, K aerogenes, S.marcescens, P. mirabilis, S. maltophilia, P. aeruginosa, A. baumannii,and A. pittii. Growth curve is observed only for the species ofStenotrophomas maltophilia. No meaningful amplification was observed fornon-target organisms.

FIG. 15. PCR assays using primers and probe disclosed in TABLE XII thattarget the gyrB gene were tested against common Gram-negative pathogens.Growth curve is observed only for the species of Stenotrophomasmaltophilia. No meaningful amplification was observed for non-targetorganisms.

FIG. 16. PCR assays using primers and probe disclosed in TABLE XIII thattarget the tuf gene were tested against common Gram-negative pathogens.Growth curve is observed only for the species of Stenotrophomasmaltophilia. No meaningful amplification was observed for non-targetorganisms.

FIG. 17. PCR assays using primers and probe disclosed in TABLE XV thattarget the rpoB gene were tested against common Gram-positive pathogens:S. agalactiae, S. pneumoniae, S. pyogenes, E. faecium, E. faecalis, S.aureus, and S. epidermidis. Growth curves are observed only forpathogens within the genus Enterococcus (E. faecium and E. faecalis). Nomeaningful amplification was observed for non-target organisms.

FIG. 18. PCR assays using primers and probes disclosed in TABLE XVI thattarget the ddl gene were tested against common Gram-positive pathogens.Growth curves are observed only for pathogens within the genusEnterococcus (E. faecium and E. faecalis). No meaningful amplificationwas observed for non-target organisms.

FIG. 19. PCR assays using primers and probe disclosed in TABLE XVIItargeting the gyrB gene were tested against common Gram-positivepathogens. Growth curves are observed only for pathogens within thegenus Enterococcus (E. faecium and E. faecalis). No meaningfulamplification was observed for non-target organisms.

FIG. 20. PCR assays using primers and probe disclosed in TABLE XVIIIthat target the CPE gene were tested against common Gram-positivepathogens: S. agalactiae, S. pneumoniae, S. pyogenes, E. faecium, E.faecalis, S. aureus, and S. epidermidis. Growth curve is observed onlyfor pathogens within the species Staphylococcus aureus. No meaningfulamplification was observed for non-target organisms.

FIG. 21. PCR assays using primers and probe disclosed in TABLE XIX thattarget the gyrB gene were tested against common Gram-positive pathogens.Growth curve is observed only for pathogens within the speciesStaphylococcus aureus. No meaningful amplification was observed fornon-target organisms.

FIG. 22. PCR assays using primers and probe disclosed in TABLE XX thattarget the ddlA gene were tested against common Gram-positive pathogens.Growth curve is observed only for pathogens within the speciesStaphylococcus aureus. No meaningful amplification was observed fornon-target organisms.

FIG. 23. PCR assays using primers and probe disclosed in TABLE XXII thattarget the gyrB gene were tested against common Gram-positive pathogens:S. agalactiae, S. pneumoniae, S. pyogenes, E. faecium, E. faecalis, S.aureus, and S. epidermidis. Growth curve is observed only for pathogenswithin the species Streptococcus agalactiae. No meaningful amplificationwas observed for non-target organisms.

FIG. 24. PCR assays using primers and probe disclosed in TABLE XXIIIthat target the sip gene were tested against common Gram-positivepathogens. Growth curve is observed only for pathogens within thespecies Streptococcus agalactiae. No meaningful amplification wasobserved for non-target organisms.

FIG. 25. PCR assays using primers and probe disclosed in TABLE XXIV thattarget the ddlA gene were tested against common Gram-positive pathogens.Growth curve is observed only for pathogens within the speciesStreptococcus agalactiae. No meaningful amplification was observed fornon-target organisms.

FIG. 26. PCR assays using primers and probe disclosed in TABLE XXVI thattarget the RDN18 (18s rRNA) gene were tested against common fungalpathogens: C. albicans and C. auris. Growth curves are observed only forpathogens within the genus Candida. Gram-negative and positive organismswere also tested and showed no meaningful amplification (data notshown).

FIG. 27. PCR assays using primers and probe disclosed in TABLE XXVIIthat target the RDN58 (5.8srRNA) gene were tested against common fungalpathogens: C. albicans and C. auris. Growth curves are observed only forpathogens within the genus Candida. Gram-negative and positive organismswere also tested and showed no meaningful amplification (data notshown).

FIG. 28. PCR assays using primers and probe disclosed in TABLE XXVIIIthat target the 16s gene were tested against common Gram-negativepathogens: E. coli, K. pneumoniae, E. cloacae, K oxytoca, K aerogenes,S. marcescens, P. mirabilis, S. maltophilia, P. aeruginosa, A.baumannii, and A. pittii. Growth curves are observed for allGram-negative pathogens.

FIG. 29. PCR assays using primers and probe disclosed in TABLE XXVIIIthat target the 16s gene were tested against common Gram-positivepathogens: S. agalactiae, S. pneumoniae, S. pyogenes, E. faecium, E.faecalis, S. aureus, and S. epidermidis. Growth curves are observed forall Gram-positive pathogens.

FIGS. 30-1 and 30-2. Established Minimum Inhibitory Concentration (MIC)breakpoints for Gram-negative bacterial organisms as determined by theClinical and Laboratory Standards Institute (CLSI) document M100 ED 30.Breakpoints are used to interpret MIC results from AntimicrobialSusceptibility Testing, and to classify “groupings” of organisms aseither Susceptible, Intermediate, or Resistant to a given antimicrobial.Groupings of organisms can be at differing levels, including, but notlimited to, species, genus, order, or a specific biochemical property.

FIG. 31. Established Minimum Inhibitory Concentration (MIC) breakpointsfor Gram-positive bacterial organisms as determined by the Clinical andLaboratory Standards Institute (CLSI) document M100 ED 30. Breakpointsare used to interpret MIC results from Antimicrobial SusceptibilityTesting, and to classify “groupings” of organisms as either Susceptible,Intermediate, or Resistant to a given antimicrobial. Groupings oforganisms can be at differing levels, including, but not limited to,species, genus, order, or a specific biochemical property.

FIG. 32. Established Minimum Inhibitory Concentration (MIC) breakpointsfor fungal organisms (yeast) as determined by the Clinical andLaboratory Standards Institute (CLSI) document M60 ED 1. Breakpoints areused to interpret MIC results from Antifungal Susceptibility Testing(AFST), and to classify “groupings” of organisms as either Susceptible,Intermediate, or Resistant to a given antifungal. Groupings of organismscan be at differing levels, including, but not limited to, species,genus, order, or a specific biochemical property. Of note is that whileAFST is recommended for Candida auris, neither CLSI or CDC currentlyhave established breakpoints for the species; instead, AFST results fromclosely related Candida spp. and expert opinion are used to determinethe susceptibility of C. auris isolates to a given antifungal.

FIG. 33. Rapid Identification and phenotypic antimicrobialsusceptibility testing of Enterobacterales utilizing three distincttarget genes (gyrB, rplP, and rpoB) and three classes of antibacterialagents: fluoroquinolone (CIP), aminoglycoside (GEN), and carbapenem(MEM).

FIG. 34. Rapid Identification and phenotypic antimicrobialsusceptibility testing of P. aeruginosa utilizing three distinct targetgenes (tuf.gyrB, rpoB) and three classes of antibacterial agents:fluoroquinolone (CIP), aminoglycoside (GEN), and carbapenem (MEM).

FIG. 35. Rapid Identification and phenotypic antimicrobialsusceptibility testing of Acinetobacter utilizing three distinct targetgenes (ompA, rpoB, and gyrB) and three classes of antibacterial agents:fluoroquinolone (CIP), aminoglycoside (GEN), and carbapenem (MEM).

FIG. 36. Rapid Identification and phenotypic antimicrobialsusceptibility testing of S. aureus utilizing three distinct targetgenes (gyrB, ddlA, tuf) and one class of antibacterial agent:cephalosporin (FOX).

FIG. 37. Rapid Identification and phenotypic antimicrobialsusceptibility testing of Enterococcus faecium utilizing three distincttarget genes (rpoB, ddl, and gyrB) and two classes of antibacterialagents: beta-lactam (AMP) and glycopeptide (VAN).

FIG. 38. Primers and Probes that target the RDN18 and RDN58 genes to beused for rapid identification and phenotypic antimicrobialsusceptibility testing of Candida.

FIG. 39. Primers and Probes that target the 16s gene to be used forrapid identification and phenotypic antimicrobial susceptibility testingof any given Gram-negative or Gram-positive bacteria.

FIG. 40A. Inclusivity and exclusivity performance of a Gram-negativepathogen PCR multiplex master mix. FIG. 40B. Breakpoint groups, channelsand dye wavelengths and names of the multiplex PCR assay.

FIG. 41A. Inclusivity and exclusivity performance of a Gram-positivepathogen PCR multiplex master mix. FIG. 41B. Breakpoint groups, channelsand dye wavelengths and names of the multiplex PCR assay.

FIG. 42. Thresholds to distinguish between susceptible and resistant canbe unique to each primer/probe set and are determined using statisticalseparation of populations as outlined in FIG. 4. The thresholdsassociated with ciprofloxacin susceptibility are shown for A)Acinetobacter baumanii (Abi), B) Enterobacteriaceae (Entero), and C)Pseudomonas aeruginosa (Pae), and are based on changes in Ct value,Relative Fluorescence Intensity (RFI), and Slope prior to the Ctfluorescence value at three different antibiotic concentrations.

FIG. 43. A) The distribution of resistant and susceptible isolates isshown for A. baumanii (Abi), E. cloacae (Ed), E. coli (Eco), K.aerogenes (Kae), K. pneumoniae (Kpn), and P. aeruginosa (Pae). B)Sensitivity, specificity, and categorical agreement for ciprofloxacinacross species using the thresholds in FIG. 42, where sensitivity andspecificity are as defined in EXAMPLE 21.

FIG. 44. Thresholds to distinguish between susceptible and resistant canbe unique to each primer/probe set and are determined using statisticalseparation of populations as outlined in FIG. 4. The thresholdsassociated with gentamicin susceptibility are shown for A) Acinetobacterbaumanii (Abi), B) Enterobacteriaceae (Entero), and C) Pseudomonasaeruginosa (Pae), and are based on Inflection cycle, changes in AbsoluteFluorescence Intensity (AFI), and Goodness of Fit for the curve fit tothe raw fluorescence data.

FIG. 45. A) The distribution of resistant and susceptible isolates isshown for A. baumanii (Abi), E. cloacae (Ed), E. coli (Eco), K.aerogenes (Kae), K. pneumoniae (Kpn), and P. aeruginosa (Pae). B)Sensitivity, specificity, and categorical agreement for gentamicinacross species using the thresholds in FIG. 44, where sensitivity andspecificity are as defined in EXAMPLE 21.

FIG. 46. Thresholds to distinguish between susceptible and resistant canbe unique to each primer/probe set and are determined using statisticalseparation of populations as outlined in FIG. 4. The thresholdsassociated with meropenem susceptibility are shown for A) Acinetobacterbaumanii (Abi), B) Enterobacteriaceae (Entero), and C) Pseudomonasaeruginosa (Pae), and are based on changes in Ct value relative to noantibiotic and the lowest antibiotic concentration, the absolute Ctvalue, and the Absolute Fluorescence Intensity (AFI).

FIG. 47. A) The distribution of resistant and susceptible isolates isshown for A. baumanii (Abi), E. cloacae (Ed), E. coli (Eco), K.aerogenes (Kae), K. pneumoniae (Kpn), and P. aeruginosa (Pae). B)Sensitivity, specificity, and categorical agreement for meropenem acrossspecies using the thresholds in FIG. 46, where sensitivity andspecificity are as defined in EXAMPLE 21.

FIG. 48. A) Workflow for testing isolates directly from positive bloodculture samples, which were created by spiking bacteria into wholeblood, separating red blood cells, inoculating plasma containingbacteria into a commercial blood culture bottle, incubating overnight,and then following standard assay workflow. B) Change in Ct values as afunction of antibiotic (Gentamicin) for various resistant andsusceptible isolates, showing that phenotypic results can be obtained onbacteria directly from positive blood culture.

FIG. 49. Polymicrobial AST where a 1:1 ratio of two Gram-negativeorganisms (Kpn and Abi) with different susceptibility combinations wereco-incubated together in the absence or presence of three differentantibiotics at varying concentrations. Each species displayed theappropriate phenotype in the corresponding detection channel asindicated by a Delta CT threshold that separates susceptible andresistant isolates, providing accurate antimicrobial susceptibilityresults for a variety of polymicrobial scenarios.

FIG. 50. Polymicrobial AST where a 1:1 ratio of one Gram-negativeorganism (Kpn) and one Gram-positive organism (Sar) with differentsusceptibility combinations were co-incubated together in the absence orpresence of three different antibiotics at varying concentrations. Eachspecies displayed the appropriate phenotype in the correspondingdetection channel as indicated by a Delta CT threshold that separatessusceptible and resistant isolates, providing accurate antimicrobialsusceptibility results for a variety of polymicrobial scenarios. N/Aindicates that there is no clinically relevant interpretation for thecorresponding bacteria-drug combination.

FIG. 51. Polymicrobial AST where a 1:1 ratio of one Gram-negativeorganism (Kpn) and one fungal organism (Cal) with differentsusceptibility combinations were co-incubated together in the absence orpresence of one antibiotic at varying concentrations. The Gram-negativespecies displayed the appropriate phenotype in the correspondingdetection channel as indicated by a Delta CT threshold that separatessusceptible and resistant isolates, providing accurate antimicrobialsusceptibility results for a variety of polymicrobial scenarios. N/Aindicates that there is no clinically relevant interpretation for thecorresponding organism-drug combination. Cal susceptibility forfluconazole is indicated.

FIG. 52. Polymicrobial AST where a 1:1 ratio of two Gram-positiveorganisms (Efs and Sar) with different susceptibility combinations wereco-incubated together in the absence or presence of one antibiotic atvarying concentrations. Both species displayed the appropriate phenotypein the corresponding detection channel as indicated by a delta-Ctthreshold that separates susceptible and resistant isolates, providingaccurate antimicrobial susceptibility results for a variety ofpolymicrobial scenarios.

FIG. 53. Polymicrobial AST where a 1:1 ratio of one Gram-positiveorganism (Sar) and one fungal organism (Cal) with differentsusceptibility combinations were co-incubated together in the absence orpresence of one antibiotic at varying concentrations. The Gram-positivespecies displayed the appropriate phenotype in the correspondingdetection channel as indicated by a delta-Ct threshold that separatessusceptible and resistant isolates, providing accurate antimicrobialsusceptibility results for a variety of polymicrobial scenarios. N/Aindicates that there is no clinically relevant interpretation for thecorresponding organism-drug combination. Cal susceptibility forfluconazole is indicated.

FIG. 54. PCR assays using primers and probes disclosed in TABLE XXXIXthat target the blaKPC, blaVIM, blaNDM, and blaOXA-48 genes were testedagainst Gram-negative pathogens with known mechanisms of carbapenemresistance. Positive (Pos) signals were observed only for the targetedresistance mechanism.

FIG. 55. PCR assays using primers and probes disclosed in TABLE XL thattarget the citC gene of P. Stuartii and invA gene of Salmonella weretested against common Gram-negative pathogens: E. coli, K pneumoniae, E.cloacae, K. oxytoca, K aerogenes, S. marcescens, P. mirabilis, C.freundii, P. stuartii, P. rettgeri, S. enterica, S. maltophilia, P.aeruginosa, A. baumannii, and A. pittii. Only species-specific growthcurves were observed. These results represent non-limiting examples ofspecies-specific detection sets that allow improved breakpoint based ASTcalling for some specific species within the order Enterobacterales.

FIG. 56. PCR assays using primers and probes disclosed in TABLE XLI thattarget gyrB gene of S. agalactiae, ddlA gene of S. agalactiae, tuf geneof S. pneumonia, and speB gene of S. pyogenes were tested against commonGram-positive pathogens: S. agalactiae, S. pneumoniae, S. pyogenes, E.faecium, E. faecalis, S. aureus, and S. epidermidis. Onlyspecies-specific growth curves were observed. These results representnon-limiting examples of species-specific detection sets that allowimproved breakpoint based AST calling for some specific species withinthe Staphylococcus and Streptococcus genera.

FIG. 57. The left panel shows the thresholds to distinguish betweensusceptible and resistant strains in an ID-AST PCR assay that utilizednon-species-specific primer/probe sets (e.g. sets that hybridize to atarget gene in the Enterobacteriales order) may be comfounded byspecies-specific differences in phenotype manifestation. The right panelshows the use of species-specific primer/probe sets that provide speciesidentification would enable separate interpretation for each individualspecies, leading to improved Categorical Agreement to CLSI standards.

FIG. 58. Data interpretation strategy wherein a sigmoidal function isfit to the raw PCR curve data followed by calculation of curveparameters and features. Features are then compared between the presenceof various antibiotic concentrations and the no-antibiotic reference toderive relative feature changes. Relative change features are then inputinto separate machine learning algorithms along with the ground truthMIC in order to train predictive models. Trained models then participateas a voting ensemble to return the final predicted MIC.

FIG. 59. Diagram indicating how Species ID, Antimicrobial SusceptibilityTesting, Resistance Mechanism detection, and Universal 16s rRNAphenotypic information is combined to return a result, wherein SpeciesID is used to select the appropriate algorithm for MIC prediction whichis then compared to the appropriate breakpoints from regulatory bodiesto determine susceptibility information.

DETAILED DESCRIPTION OF THE INVENTION Definitions

The disclosed methods may include performing at least one cycling stepthat includes amplifying one or more portions of the nucleic acidmolecule gene target from a sample using one or more pairs of primers. A“sample” or “biological sample” as used herein refers to a sample thatincludes but is not limited to whole blood, plasma, serum, red bloodcell fraction, saliva, cerebrospinal fluid, semen, stool, urine, rectalswab, bile, lymph, sputum, lavage fluid, or a combination thereof“Primer(s)” as used herein refer to oligonucleotide primers thatspecifically anneal to the target bacterial gene, and initiate DNAsynthesis therefrom under appropriate conditions producing therespective amplification products. Each of the discussed primers annealsto a target within or adjacent to the respective target nucleic acidmolecule such that at least a portion of each amplification productcontains nucleic acid sequence corresponding to the target. The one ormore amplification products are produced provided that one or more ofthe target bacterial gene nucleic acid is present in the sample, thusthe presence of the one or more of target bacterial gene amplificationproducts is indicative of the presence of that bacterial strain in thesample. The amplification product should contain the nucleic acidsequences that are complementary to one or more detectable probes fortarget bacterial gene. “Probe(s)” as used herein refer tooligonucleotide probes that specifically anneal to nucleic acid sequenceencoding the target bacterial gene. Each cycling step includes anamplification step, a hybridization step, and a detection step, in whichthe sample is contacted with the one or more detectable probes fordetection of the presence or absence of the bacterial strain in thesample.

As used herein, the term “amplifying” refers to the process ofsynthesizing nucleic acid molecules that are complementary to one orboth strands of a template nucleic acid molecule. Amplifying a nucleicacid molecule typically includes denaturing the template nucleic acid,annealing primers to the template nucleic acid at a temperature that isbelow the melting temperatures of the primers, and enzymaticallyelongating from the primers to generate an amplification product.Amplification typically requires the presence of deoxyribonucleosidetriphosphates, a DNA polymerase enzyme (e.g., Platinum® Taq) and anappropriate buffer and/or co-factors for optimal activity of thepolymerase enzyme (e.g., MgCl₂ and/or KCl).

The term “primer” as used herein is known to those skilled in the artand refers to oligomeric compounds, primarily to oligonucleotides butalso to modified oligonucleotides that are able to “prime” DNA synthesisby a template-dependent DNA polymerase, i.e., the 3′-end of the, e.g.,oligonucleotide provides a free 3′-OH group whereto further“nucleotides” may be attached by a template-dependent DNA polymeraseestablishing 3′ to 5′ phosphodiester linkage whereby deoxynucleosidetriphosphates are used and whereby pyrophosphate is released. Therefore,there is—except possibly for the intended function—no fundamentaldifference between a “primer”, an “oligonucleotide”, or a “probe”.

The term “hybridizing” refers to the annealing of one or more probes toan amplification product. Hybridization conditions typically include atemperature that is below the melting temperature of the probes but thatavoids non-specific hybridization of the probes.

The term “5′ to 3′ nuclease activity” refers to an activity of a nucleicacid polymerase, typically associated with the nucleic acid strandsynthesis, whereby nucleotides are removed from the 5′ end of nucleicacid strand.

The term “thermostable polymerase” refers to a polymerase enzyme that isheat stable, i.e., the enzyme catalyzes the formation of primerextension products complementary to a template and does not irreversiblydenature when subjected to the elevated temperatures for the timenecessary to effect denaturation of double-stranded template nucleicacids.

Generally, the synthesis is initiated at the 3′ end of each primer andproceeds in the 5′ to 3′ direction along the template strand.Thermostable polymerases have been isolated from Thermus flavus, T.ruber, T. thermophilus, T. aquaticus, T. lacteus, T. rubens, Bacillusstearothermophilus, and Methanothermus fervidus. Nonetheless,polymerases that are not thermostable also can be employed in PCR assaysprovided the enzyme is replenished.

The term “complement thereof” refers to nucleic acid that is both thesame length as, and exactly complementary to, a given nucleic acid.

The term “extension” or “elongation” when used with respect to nucleicacids refers to when additional nucleotides (or other analogousmolecules) are incorporated into the nucleic acids. For example, anucleic acid is optionally extended by a nucleotide incorporatingbiocatalyst, such as a polymerase that typically adds nucleotides at the3′ terminal end of a nucleic acid.

The terms “identical” or percent “identity” in the context of two ormore nucleic acid sequences, refer to two or more sequences orsubsequences that are the same or have a specified percentage ofnucleotides that are the same, when compared and aligned for maximumcorrespondence, e.g., as measured using one of the sequence comparisonalgorithms available to persons of skill or by visual inspection.Exemplary algorithms that are suitable for determining percent sequenceidentity and sequence similarity are the BLAST programs, which aredescribed in, e.g., Altschul et al. (1990) “Basic local alignment searchtool” J. Mol. Biol. 215:403-410, Gish et al. (1993) “Identification ofprotein coding regions by database similarity search” Nature Genet.3:266-272, Madden et al. (1996) “Applications of network BLAST server”Meth. Enzymol. 266:131-141, Altschul et al. (1997) “Gapped BLAST andPSI-BLAST: a new generation of protein database search programs” NucleicAcids Res. 25:3389-3402, and Zhang et al. (1997) “PowerBLAST: A newnetwork BLAST application for interactive or automated sequence analysisand annotation” Genome Res. 7:649-656, which are each incorporatedherein by reference.

A “modified nucleotide” in the context of an oligonucleotide refers toan alteration in which at least one nucleotide of the oligonucleotidesequence is replaced by a different nucleotide that provides a desiredproperty to the oligonucleotide. Exemplary modified nucleotides that canbe substituted in the oligonucleotides described herein include, e.g., aC5-methyl-dC, a C5-ethyl-dC, a C5-methyl-dU, a C5-ethyl-dU, a2,6-diaminopurine, a C5-propynyl-dC, a C5-propynyl-dU, a C7-propynyl-dA,a C7-propynyl-dG, a C5-propargylamino-dC, a C5-propargylamino-dU, aC7-propargylamino-dA, a C7-propargylamino-dG, a7-deaza-2-deoxyxanthosine, a pyrazolopyrimidine analog, a pseudo-dU, anitro pyrrole, a nitro indole, 2′-0-methyl Ribo-U, 2′-0-methyl Ribo-C,an N4-ethyl-dC, an N6-methyl-dA, and the like. Many other modifiednucleotides that can be substituted in the oligonucleotides are referredto herein or are otherwise known in the art. In certain embodiments,modified nucleotide substitutions modify melting temperatures (Tm) ofthe oligonucleotides relative to the melting temperatures ofcorresponding unmodified oligonucleotides. To further illustrate,certain modified nucleotide substitutions can reduce non-specificnucleic acid amplification (e.g., minimize primer dimer formation or thelike), increase the yield of an intended target amplicon, and/or thelike in some embodiments. Examples of these types of nucleic acidmodifications are described in, e.g., U.S. Pat. No. 6,001,611, which isincorporated herein by reference.

The term “TAGS” or “Temperature Assisted Generation of Signal”(disclosed in U.S Patent Publication No. 2018/0073064 and incorporatedby reference herein in its entirety) is a multiplexing technology thatenables the measurement of multiple individual targets in eachfluorescence channel by collecting fluorescence data at differenttemperatures during thermal cycling. Consequently, TAGS multiplexingwith two or three temperature channels can double or triple the numberof resolvable targets per optical channel. In principle, this technologycan be deployed on any quantitative PCR (qPCR) instrument capable ofcollecting more than one fluorescence read per PCR cycle.

The term “colonization” is defined as the presence of bacteria or fungion a body surface (like on the skin, mouth, intestines or airway)without necessarily causing disease in the person. The term “infection”is defined as the invasion of a host organism's bodily tissues bydisease-causing organisms (such as bacteria and fungi). Infection alsoresults from the interplay between pathogens and the defenses of thehosts they infect.

The term “antimicrobial” refers to an agent or drug used to treat amicrobial infection, usually by killing the microorganism or byinhibiting its growth. Antimicrobials may include antibiotics fortreating bacterial infection, antifungals for treating fungi infection,antiprotozoals for treating protozoan infection and antivirals fortreating viral infection. Antimicrobials are classified in severaldifferent manners (and referred as “antimicrobial class”) and includeclassification by mechanism of action (e.g. inhibition of cell wallsynthesis, inhibition of protein or nucleic acid synthesis, disruptionof cell membrane), by source (e.g. from natural sources or synthetic),and by chemical structure (e.g. □-lactams, aminoglycosides, macrolides,quinolones etc.).

Examples of antimicrobial classes include but are not limited to:Allylamines, Amidinopenicillins, Aminocyclitols, Aminoglycosides,Amphenicols, Ansamycins, B-3-Glucan synthase inhibitors, Carbapenems,Cephalosporins, Clycylcyclines, Cyclic polypeptides, Glycopeptides,Imidazoles, Lincosamides, Lipopeptides, Macrolides and ketolides,Monobactams, Nitrofurantoins, Nitroimidazoles, Oxazolidinones,Penicillins, Phophonic acid derivatives, Pleuromutilins, Polyenes,Polymyxins, Pseudomonic acids, Quinolones, Riminofenazines, Steroidantibacterials, Streptogramins, Sulfonamides, dihydrofolate reductaseinhibtors and combinations, Sulfones, Tetracyclines, and Triazoles.

Examples of antimicrobial drugs or agents include but are not limitedto: naftifine, mecillinam, spectinomycin, chloramphenicol, rifampicin,caspofungin, meropenem, ceftriaxone, cefepime, ceftaroline, tigecycline,bacitracin, vancomycin, miconazole, clindamycin, daptomycin,erythromycin, telithromycin, aztreonam, nitrofurantoin, metronidazole,linezolid, ampicillin, fosfomycin, retapamulin, amphotericin-B,colistin, mupirocin, ciprofloxacin, clofazimine, fusidic acid,quinupristin/dalfopristin, sulfamethoxazole, trimethoprim, dapsone,chlortetracycline, and fluconazole.

The term “the presence of at least one concentration” when applied to anantimicrobial/antifungal or a class of antimicrobials/antifungals refersto given concentration(s) of the antimicrobial/antifungal or the classof antimicrobials/antifungals that is/are present at value(s) thatis/are not zero.

The term “Minimum Inhibitory Concentration” or “MIC” refers to thelowest concentration of an antimicrobial required to inhibit the growthof an organism. In classical culture-based tests, the MIC is determinedwhen the bacteria are added to wells containing growth media and varyingconcentrations of the antimicrobial. The concentration of antimicrobialis doubled in each successive well and the MIC is found by identifyingthe well with the lowest antimicrobial concentration in which there isno visible growth after an incubation period. The term “breakpoint”refers to a chosen concentration of an antimicrobial that defineswhether a species of bacteria is susceptible or resistant to theantimicrobial. If the MIC is less than or equal to the susceptibilitybreakpoint the bacteria is considered susceptible to the antimicrobial.If the MIC is greater than this value the bacteria is consideredintermediate or resistant to the antimicrobial. Breakpoints cantherefore be used to interpret MIC results from AntimicrobialSusceptibility Testing, and to classify “groupings” of organisms aseither “Susceptible, Intermediate, or Resistant (SIR)” to a givenantimicrobial or antifungal.

Breakpoints are an integral part of modern microbiology laboratorypractice and are used to define susceptibility and resistance toantibacterials. Depending on the testing method, they are expressed aseither a concentration (in mg/liter or μg/ml) or a zone diameter (inmm). In general, all susceptibility testing methods require breakpoints,also known as interpretive criteria, so that the results of the testscan be interpreted as susceptible, intermediate, or resistant andreported as such to a broad range of clinicians. “Clinical breakpoints”which refer to those concentrations (MICs) that separate strains wherethere is a high likelihood of treatment success from those bacteriawhere treatment is more likely to fail. In their simplest form, thesebreakpoints are derived from prospective human clinical studiescomparing outcomes with the MICs of the infecting pathogen.

Detection and Identification of Infectious Pathogens

The present disclosure provides methods to detect infectious pathogens,for example, bacteria strains that cause bloodstream infections. Themethods comprise the steps of amplifying portions of target genes by PCRusing strain-specific, species-specific, genus-specific,family-specific, or order-specific primer sequences and detecting theamplification products using strain-specific, species-specific,genus-specific, family-specific, or order-specific probe nucleic acidsequences. Target gene selection was the result of an in silico searchof the public sequence database, as well as a literature search fornucleic acid sequences that are specific to a species (e.g. E. coli) orto an order (e.g. Enterobacterales) and discriminate against otherstrains and families. As a result of the search, the following targetgenes were identified:

Enterobacterales Order: rplP, ompA, tuf, gyrB, rpoBEnterobacteriaceae family: rplP, ompA, tuf, gyrB, rpoBEnterococcus genus: tuf, rpoB, sodA, ddl, gyrBPseudomonas genus: gyrB, 0-antigen acetylase, rpoB, ecfX, tufAcinetobacter genus: ompA, tusA, rpoB, gyrBStrenotrophomonas maltophilia: fdnG, gyrB, tufStaphylococcus aureus: CPE, gyrB, nuc, rpoB, tuf, ddlAStaphylococcus epidermidis: altE, femACoagulase-negative Staphylococci: rpoB, tuf, sodAStreptococcus genus: tuf, gyrB, sip, ddlAStreptococcus pneumoniae: lytA, SP2020, piaBProteus mirabilis: UreR, UreCCandida albicans: ACT, RPB-1, 5.8s ribosomal RNA, 18s ribosomal RNA

For detection of bacteria belonging to the Enterobacterales Order or tothe Enterobacteriaceae family, primers and probes to amplify the rplPgene encoding for the ribosomal L16 protein are provided (SEQ ID NO:1-3, TABLE I). Addition of a second probe (SEQ ID NO: 4, TABLE I)further extends inclusivity to include other prevalent pathogens in theorder Enterobacterales, such as the strains Serratia marcescens andProteus mirabilis. Nucleic acids other than those exemplified herein canalso be used to detect highly specific pathogen grouping target genes ina sample. For example, functional variants can be evaluated forspecificity and/or sensitivity by those of skill in the art usingroutine methods. Representative functional variants can include, e.g.,one or more deletions, insertions, and/or substitutions in the targetgene primers and probes disclosed herein. More specifically, embodimentsof the oligonucleotides each include a nucleic acid with a sequenceselected from SEQ ID NOs: 1-4, a substantially identical variant thereofin which the variant has at least, e.g., 80%, 90%, or 95% sequenceidentity to one of SEQ ID NOs: 1-4, or a complement of SEQ ID NOs: 1-4and the variant.

TABLE IOligonucleotides for detecting Enterobacteriaceae family or EnterobacteralesorderPrimers and Probes that hybridize to rplP gene in Enterobacteriaceae/Enberbacteriales strains Oligonucleotide Oligonucleotide SEQ ID TypeName NO: Sequence Modifications Forward primer RM_ENTF 1TAATCGGCAGTTTCGCTG<t_BB_ t_BB_dC = dC> t-butylbenzyl-dC Reverse primerRM_ENTRP 2 GTTCCCGGACAAACCGATC<t_ t_BB_dA = BB_dA> t-butylbenzyl-dAProbe 1 RM_ETP02 3 <Cy5.5>TTCACGGGCCA<BHQ_2> <Cy5.5>:GCTCTTCCGGAACACCGTCCA Fluorophore T<Phos> <BHQ_2>: Quencher<Phos>: Phosphate Probe 2 RM_ETP02B 4 <Cy5.5>CTGGATCAGGG<BHQ_2> <Cy5.5>:CAACCCAATACTCCACGTTACC Fluorophore <Phos> <BHQ_2>: Quencher<Phos>: Phosphate

The detection of bacteria belonging to the Enterobacterales order canalso comprise of other primers and probes for amplifying the rplP gene(SEQ ID NOs: 5-7, TABLE II), as well as primers and probes foramplifying the gyrB gene that encodes the DNA gyrase subunit B protein(SEQ ID NOs: 8-10, TABLE III) and primers and probes for amplifying therpoB gene that encodes the DNA-dependent RNA polymerase (SEQ ID NOs:11-16, TABLE IV). Representative functional variants can include, e.g.,one or more deletions, insertions, and/or substitutions in the targetgene primers and probes disclosed herein. More specifically, embodimentsof the oligonucleotides each include a nucleic acid with a sequenceselected from SEQ ID NOs: 5-7, 8-10, 11-16, a substantially identicalvariant thereof in which the variant has at least, e.g., 80%, 90%, or95% sequence identity to one of SEQ ID NOs: 5-7, 8-10, 11-16, or acomplement of SEQ ID NOs: 5-7, 8-10, 11-16 and the variant.

TABLE II Oligonucleotides for detecting Enterobacterales orderPrimers and Probes that hybridize to rplP gene in Enterobacteriaceae/Enterobacterales strains Oligonucleotide Oligonucleotide SEQ ID TypeName NO: Sequence Modifications Forward primer SEGP2891 5AATTCCGTAAAATGCACAAAG GCC Reverse primer SEGP2892 6GCTTAACTGCACGGGTCATAG CA Probe SEGP2893 7 <FAM>TGGTCGTCT<ZEN>GAC<FAM>: Fluorophore TGCACGTCAGATCGAAGC <ZEN>: Quencher <3IABkFQ><3IABkFQ>: 3′ Blocker

TABLE III Oligonucleotides for detecting Enterobacterales orderPrimers and Probes that hybridize to gyrB gene in Enterobacteriaceae/Enterobacterales strains Oligonucleotide Oligonucleotide SEQ ID TypeName NO: Sequence Modifications Forward primer SEGP1899 8TGTCGAATTCTTATGACTCCTC CAGTA Reverse primer SEGP1901 9 CGCGAGCGCTTCGTCGAProbe SEGP2016 10 <HEX>CCGGTCTGC<ZEN>ACC <HEX>: FluorophoreACATGGTATTCGAGGTGG <ZEN>: Quencher <3IABkFQ> <3IABkFQ>: 3′ Blocker

TABLE IV Oligonucleotides for detecting Enterobacterales orderPrimers and Probes that hybridize to rpoB gene in Enterobacteriaceae/Enterobacterales strains Oligonucleotide Oligonucleotide SEQ ID TypeName NO: Sequence Modifications Forward primer SEGP2799 11TGGTAAACGTCCACAAGTTCTGGA Reverse primers SEGP2800 12CATACTGCCCTTCAGGATCTTGC SEGP2802 13 GTAGCTGACATATTGCAGTTCAGCA SEGP282114 CCGTTCTGACCGTCCGGATC Probes SEGP2804 15 <FAM>TATCTCCTT<ZEN>TCTA<FAM>: Fluorophore TCCAGCTTGACTCGTTTC AGA <ZEN>: QuencherAGTTTATCGA<3IABkFQ> <3IABkFQ>: 3′ Blocker SEGP2822 16<FAM>TC TCC TTTC<ZEN>T ATCCAGCTGGATTCATTC CAG AAATTCATTGAAC<3IABkFQ>

For detection of bacteria belonging to the species Acinetobacterbaumannii (Abi), primers and probes for amplifying the ompA geneencoding for the outer membrane protein A are provided (see TABLE V).Nucleic acids other than those exemplified herein can also be used todetect Acinetobacter genus-specific pathogen grouping target genes in asample. For example, functional variants can be evaluated forspecificity and/or sensitivity by those of skill in the art usingroutine methods. Representative functional variants can include, e.g.,one or more deletions, insertions, and/or substitutions in the targetgene primers and probes disclosed herein. More specifically, embodimentsof the oligonucleotides each include a nucleic acid with a sequenceselected from SEQ ID NOs: 17-19, 20-22, 29-31 a substantially identicalvariant thereof in which the variant has at least, e.g., 80%, 90%, or95% sequence identity to one of SEQ ID NOs: 17-19, 20-22, 29-31 or acomplement of SEQ ID NOs: 17-19, 20-22, 29-31 and the variant.

TABLE V Oligonucleotides for detecting Acinetobacter baumanniiPrimers and Probes that hybridize to ompA gene in A. baumanniiOligonucleotide Oligonucleotide SEQ ID Type Name NO: SequenceModifications Forward primer RM_AFP01 17 TTGGTGGTCACTTGAAG<t_BB_t_BB_dC = dC> t-butylbenzyl-dC Reverse primer RM_ARP02 18TTTCTGGCTTGTATTGGT<t_BB_ t_BB_dC = dC> t-butylbenzyl-dC Probe RM_P02 19<HEX_Thr>ACTCCAG<BHQ_2>T < HEX_Thr >: TGCTCCACAACCACAAGAG<Phos>Fluorophore <BHQ_2>: Quencher <Phos>: Phosphate Forward primer SEGP260320 TTATCTTTAGCTCGTGCTAACTC TGTTAAA Reverse primer SEGP2606 21GCACGACCTTCTTTAGTTTTGTT GTCA Probe SEGP2769 22 <ATTO>TCTACTCA<BHQ_2>AG<ATTO>: GTTTCGCTTGGGATCAACCGAT Fluorophore TGCT<Phos> <BHQ_2>: Quencher<Phos>: Phosphate Forward primer SEGP1813 29 ACCCTAACGCTACTGCACGTReverse primer SEGP1815 30 GGTTGATCCCAAGCGAAACCT Probe SEGP1951 31<ATTO>TCGAAGGT<BHQ_2>CA <ATTO>: CACAGATAACACT<Phos> Fluorophore <BHQ_2>:Quencher <Phos>: Phosphate

The detection of Acinetobacter baumannii can also comprise of primersand probes for amplifying the rpoB gene (SEQ ID NOs: 23-25, TABLE VI)and for amplifying the gyrB gene (SEQ ID NOs: 26-28, TABLE VII).Representative functional variants can include, e.g., one or moredeletions, insertions, and/or substitutions in the target gene primersand probes disclosed herein. More specifically, embodiments of theoligonucleotides each include a nucleic acid with a sequence selectedfrom SEQ ID NOs: 23-25, 26-28, a substantially identical variant thereofin which the variant has at least, e.g., 80%, 90%, or 95% sequenceidentity to one of SEQ ID NOs: 23-25, 26-28, or a complement of SEQ IDNOs: 23-25, 26-28, and the variant.

TABLE VI Oligonucleotides for detecting Acinetobacter baumanniiPrimers and Probes that hybridize to rpoB gene in Acinetobacter baumanniiOligonucleotide Oligonucleotide SEQ ID Type Name NO: SequenceModifications Forward primer SEGP2590 23 CATACTCATATACCGAAAAGAAACGGReverse primer SEGP2593 24 CTATACTCAACAAATTCTAAAGCAGC Probe SEGP2594 25<FAM>CGCGAAGAT<ZEN>ATCGGTCT <FAM>: CC<3IABkFQ> Fluorophore<ZEN>: Quencher <3IABkFQ>: 3′ Blocker

TABLE VII Oligonucleotides for detecting Acinetobacter baumanniiPrimers and Probes that hybridize to gyrB gene in Acinetobacter baumanniiOligonucleotide Oligonucleotide SEQ ID Type Name NO: SequenceModifications Forward primer SEGP2626 26 ACAGAACAAACCAATGAAAAGGCTTATGATTC Reverse primer SEGP2628 27 ACCATATGGTGTAAACCGGTACC ProbeSEGP2629 28 <FAM>AAAGTATTA<ZEN>CGTGATTA <FAM>: GATGCAGTTCGTAAACGTCCGGGTFluorophore <3IABkFQ> <ZEN>: Quencher <3IABkFQ>: 3′ Blocker

For detection of bacteria belonging to the species Pseudomonasaeruginosa (Pae), primers and probes for amplifying the tuf geneencoding elongation factor (SEQ ID NOs: 32-34, TABLE VIII), the gyrBgene (SEQ ID NOs: 35-37, TABLE IX) and the rpoB gene (SEQ ID NOs: 38-40,TABLE X) are provided. Nucleic acids other than those exemplified hereincan also be used to detect Pseudomonas genus-specific pathogen groupingtarget genes in a sample. For example, functional variants can beevaluated for specificity and/or sensitivity by those of skill in theart using routine methods. Representative functional variants caninclude, e.g., one or more deletions, insertions, and/or substitutionsin the target gene primers and probes disclosed herein. Morespecifically, embodiments of the oligonucleotides each include a nucleicacid with a sequence selected from SEQ ID NOs: 32-34, 35-37, 38-40, asubstantially identical variant thereof in which the variant has atleast, e.g., 80%, 90%, or 95% sequence identity to one of SEQ ID NOs:32-34, 35-37, 38-40, or a complement of SEQ ID NOs: 32-34, 35-37, 38-40and the variant.

TABLE VIII Oligonucleotides for detecting Pseudomonas aeruginosaPrimers and Probes that hybridize to tuf gene in Pseudomonas aeruginosaOligonucleotide Oligonucleotide SEQ Type Name ID NO: SequenceModifications Forward primer SEGP2341 32 CCGTGCAGAAGCTGGTAGReverse primer SEGP2342 33 GAGATCGAGAACACGTCTTCG Probe SEGP2343 34<FAM>TTCCGGAGC<ZEN>CGGTTCGT <FAM>: GCCATCG<3IABkFQ> Fluorophore<ZEN>: Quencher <3IABkFQ>: 3′ Blocker

TABLE IX Oligonucleotides for detecting Pseudomonas aeruginosaPrimers and Probes that hybridize to gyrB gene in Pseudomonas aeruginosaOligonucleotide Oligonucleotide SEQ Type Name ID NO: SequenceModifications Forward primer SEGP2630 35 GGAGTACAACATCGACAAGCTGCReverse primer SEGP2631 36 CGCTCGATCAGCTCGGGC Probe SEGP2632 37<FAM>CACAACATC<ZEN>ATCATCATG <FAM>: ACCGATGCTGACGTCGAC<3IABkFQ>Fluorophore <ZEN>: Quencher <3IABkFQ>: 3′ Blocker

TABLE X Oligonucleotides for detecting Pseudomonas aeruginosaPrimers and Probes that hybridize to rpoB gene in Pseudomonas aeruginosaOligonucleotide Oligonucleotide SEQ Type Name ID NO: SequenceModifications Forward primer SEGP2634 38 GGCGTGCTGAAGATCGTCAAReverse primer SEGP2637 39 ACCGGCATGATCACCGAGA Probe SEGP2640 40<FAM>CGCATCCAG<ZEN>CCGGGC <FAM>: GACAAGATGG<3IABkFQ> Fluorophore<ZEN>: Quencher <3IABkFQ>: 3′ Blocker

For detection of bacteria belonging to the species Strenotrophomonasmaltophilia (S. maltophilia), primers and probes for amplifying the fdnGgene (SEQ ID NOs: 41-43, TABLE XI), the gyrB gene (SEQ ID NOs: 44-46,TABLE XII) and the tuf gene (SEQ ID NOs: 47-49, TABLE XIII) areprovided. Nucleic acids other than those exemplified herein can also beused to detect Strenotrophomonas genus-specific pathogen grouping targetgenes in a sample. For example, functional variants can be evaluated forspecificity and/or sensitivity by those of skill in the art usingroutine methods. Representative functional variants can include, e.g.,one or more deletions, insertions, and/or substitutions in the targetgene primers and probes disclosed herein. More specifically, embodimentsof the oligonucleotides each include a nucleic acid with a sequenceselected from SEQ ID NOs: 41-43, 44-46, 47-49, a substantially identicalvariant thereof in which the variant has at least, e.g., 80%, 90%, or95% sequence identity to one of SEQ ID NOs: 41-43, 44-46, 47-49, or acomplement of SEQ ID NOs: 41-43, 44-46, 47-49, and the variant.

TABLE XI Oligonucleotides for detecting Strenotrophomonas maltophiliaPrimers and Probes that hybridize to fdnG gene in Strenotrophomonas maltophiliaOligonucleotide Oligonucleotide SEQ Type Name ID NO: SequenceModifications Forward primer SEGP2532 41 CCAAGCTCGACAAGCCGTACReverse primer SEGP2538 42 GCTTGGAGAACGCGCTGATC Probe SEGP2544 43<FAM>TGCAGGCGT<ZEN>A <FAM>: Fluorophore CGAGCTGATGAACGAAGGC<ZEN>: Quencher <3IABkFQ> <3IABkFQ>: 3′ Blocker

TABLE XII Oligonucleotides for detecting Strenotrophomonas maltophiliaPrimers and Probes that hybridize to gyrB gene in Strenotrophomonas maltophiliaOligonucleotide Oligonucleotide SEQ Type Name ID NO: SequenceModifications Forward primer SEGP2578 44 TGCAGTGGACCGACTCCTAReverse primer SEGP2579 45 CTGCTTGGCGATGCCGTTCT Probe SEGP2580 46<FAM>GACGATGTA<ZEN>CTGC <FAM>: Fluorophore TTCACCAAC<3IABkFQ><ZEN>: Quencher <3IABkFQ>: 3′ Blocker

TABLE XIII Oligonucleotides for detecting Strenotrophomonas maltophiliaPrimers and Probes that hybridize to tuf gene in Strenotrophomonas maltophiliaOligonucleotide Oligonucleotide SEQ Type Name ID NO: SequenceModifications Forward primer SEGP2572 47 GCACCAAGCCGCACGTCAReverse primer SEGP2573 48 GTGCGCGGTCGAGATCGT Probe SEGP2574 49<FAM>CAAGACCAC<ZEN>GG <FAM>: Fluorophore TGACCGC<3IABkFQ><ZEN>: Quencher <3IABkFQ>: 3′ Blocker

For detection of bacteria belonging to the Enterococcus genus, primersand probes for amplifying the tuf gene (SEQ ID NOs: 50-52, TABLE XIV),the rpoB gene (SEQ ID NOs: 53-55, TABLE XV), the ddl gene encoding xxxx(SEQ ID NOs: 56-61, TABLE XVI), and the gyrB gene (SEQ ID NOs: 62-66,TABLE XVII) are provided. Nucleic acids other than those exemplifiedherein can also be used to detect Enterococcus genus-specific pathogengrouping target genes in a sample. For example, functional variants canbe evaluated for specificity and/or sensitivity by those of skill in theart using routine methods. Representative functional variants caninclude, e.g., one or more deletions, insertions, and/or substitutionsin the target gene primers and probes disclosed herein. Morespecifically, embodiments of the oligonucleotides each include a nucleicacid with a sequence selected from SEQ ID NOs: 50-52, 53-55, 56-61,62-66, a substantially identical variant thereof in which the varianthas at least, e.g., 80%, 90%, or 95% sequence identity to one of SEQ IDNOs: 50-52, 53-55, 56-61, 62-66, or a complement of SEQ ID NOs: 50-52,53-55, 56-61, 62-66 and the variant.

TABLE XIV Oligonucleotides for detecting Enterococcus genusPrimers and Probes that hybridize to tuf gene in Enterococcus genusOligonucleotide Oligonucleotide SEQ Type Name ID NO: SequenceModifications Forward primer SEGP1632 50 GACAAACCATTCATGATGCCAGReverse primer SEGP1631 51 AACTTCGTCACCAACGCGAAC Probe SEGP1633 52<HEX>CTGGACGTG<ZEN>GTA <HEX>: Fluorophore CTGTTGCTAC<3IABkFQ><ZEN>: Quencher <3IABkFQ>: 3′ Blocker

TABLE XV Oligonucleotides for detecting Enterococcus genusPrimers and Probes that hybridize to rpoB gene in Enterococcus genusOligonucleotide Oligonucleotide SEQ Type Name ID NO: SequenceModifications Forward primer SEGP2522 53 CCGTCCAGTGGTAGCAAGTAT CAReverse primer SEGP2525 54 ACCATAGTGAGAGTAGTGAAC GTCA Probe SEGP2770 55<HEX>TTGACTCGT<ZEN>GA <HEX>: Fluorophore CCGTGCCGGTTATGAAGTTCG<ZEN>: Quencher <3IABkFQ> <3IABkFQ>: 3′ Blocker

TABLE XVI Oligonucleotides for detecting Enterococcus genusPrimers and Probes that hybridize to ddl gene in Enterococcus genusOligonucleotide Oligonucleotide SEQ Type Name ID NO: SequenceModifications Forward primer SEGP1624 56 CGTAGCATTCTATGATTATGAAGCCSEGP1627 57 GACAGGAAAGAAACTAGGAGGAC Reverse primer SEGP1625 58CATCGTGTAAGCTAACTTCG SEGP1628 59 AAACAGACACATCGTGCT Probe SEGP1626 60<HEX>CAGATTCCA<ZEN>GCCGAA <HEX>: Fluorophore SEGP1629 61 GTGCC<3IABkFQ><ZEN>: Quencher <HEX>CACTTCTGC<ZEN>CGCCAT <3IABkFQ>: 3′ ACAACAA<3IABkFQ>Blocker

TABLE XVII Oligonucleotides for detecting Enterococcus genusPrimers and probes that hybridize to gyrB gene in Enterococcus genusOligonucleotide Oligonucleotide SEQ Type Name ID NO: SequenceModifications Forward primer SEGP2882 62 AGCAACGATCCTGAAAAATGCGAATTGTTCATC SEGP2884 63 AGTAAAGATCCGGAAAAATGCGAA TTATTTATC Reverse primerSEGP2885 64 AAAGACCGGATCTCTTCATTTGCC SEGP2886 65AATGACCGAATTTCTTCATTGGCT Probe SEGP2888 66 <FAM>CCAATTCGT<ZEN>GGGAA<FAM>: Fluorophore AATCTTGAATGTTGAGAAAGCAAG <ZEN>: Quencher CA<3IABkFQ><3IABkFQ>: 3′ Blocker

For detection of bacteria belonging to the species Staphylococcus aureus(S. aureus), primers and probes for amplifying the CPE gene encoding aprotein involved in capsular formation (SEQ ID NOs: 67-69, 72 TABLEXVIII), the gyrB gene (SEQ ID NOs: 73-75, TABLE XIX), the ddlA gene (SEQID NOs: 76-78, TABLE XX). For detection of bacteria belonging to theStaphylococcus genus, primers and probes for amplifying the tuf gene(SEQ ID NOs: 79-81, TABLE XXII) are provided. Nucleic acids other thanthose exemplified herein can also be used to detect Staphylococcusgenus-specific pathogen grouping target genes in a sample. For example,functional variants can be evaluated for specificity and/or sensitivityby those of skill in the art using routine methods. Representativefunctional variants can include, e.g., one or more deletions,insertions, and/or substitutions in the target gene primers and probesdisclosed herein. More specifically, embodiments of the oligonucleotideseach include a nucleic acid with a sequence selected from SEQ ID NOs:67-69, 72, 73-75, 76-78, 79-81, a substantially identical variantthereof in which the variant has at least, e.g., 80%, 90%, or 95%sequence identity to one of SEQ ID NOs: 67-69, 72, 73-75, 76-78, 79-81,or a complement of SEQ ID NOs: 67-69, 72, 73-75, 76-78, 79-81 and thevariant.

TABLE XVIII Oligonucleotides for detecting Staphylococcus aureusPrimers and Probes that hybridize to CPE gene in Staphylococcus aureusOligonucleotide Oligonucleotide SEQ Type Name ID NO: SequenceModifications Forward primer SEGP1490 67 AAGATAAGCTTATTGAACAAGG ACATCReverse primer SEGP1491 68 CTTGAGGTGAATTGTTGTGAAC C Probe SEGP1492 72<FAM>TTAGGAATC<ZEN>AAT <FAM>: Fluorophore TATGGAAGTCGACCTCGT<ZEN>: Quencher <3IABkFQ> <3IABkFQ>: 3′ Blocker Probe SEGP1493 69<HEX>TTAGGAATC<ZEN>AAT <HEX>: Fluorophore TATGGAAGTCGACCTCGT<ZEN>: Quencher <3IABkFQ> <3IABkFQ>: 3′ Blocker

TABLE XIX Oligonucleotides for detecting Staphylococcus aureusPrimers and Probes that hybridize to gyrB gene in Staphylococcus aureusOligonucleotide Oligonucleotide SEQ Type Name ID NO: SequenceModifications Forward primer SEGP2792 73 CACAAGTCGCACGTACAGTGReverse primer SEGP2793 74 ATTCTTCAGGACTTTTACTAGAG CAATCG Probe SEGP279475 <FAM>TAAATCAGC<ZEN>GTTA <FAM>: Fluorophore GATGTAGCAAGTC<3IABkFQ><ZEN>: Quencher <3IABkFQ>: 3′ Blocker

TABLE XX Oligonucleotides for detecting Staphylococcus aureusPrimers and Probes that hybridize to ddlA gene in Staphylococcus aureusOligonucleotide Oligonucleotide SEQ Type Name ID NO: SequenceModifications Forward primer SEGP2932 76 ATCTACTGATGAGCTTCATTTAGAAAATGGA Reverse primer SEGP2933 77 TCAAAAAGTCCTTGAATCGTG CCA ProbeSEGP2935 78 <FAM>CGCTTGAGA<ZEN>TT <FAM>: FluorophoreTCACAGCTATTGAAAGAAAGT <ZEN>: Quencher AGTTCAGGACAA<3IABkFQ><3IABkFQ>: 3′ Blocker

TABLE XXI Oligonucleotides for detecting Staphylococcus GenusPrimers and Probes that hybridize to tuf gene in Staphylococcus genusOligonucleotide Oligonucleotide SEQ Type Name ID NO: SequenceModifications Forward primer SEGP1835 79 CCGTGTTGAACGTGGTCAAAT CAAAReverse primer SEGP1836 80 AGCAGCTAATACTTGACCACG TTGTA Probe SEGP1838 81<FAM>AGACTACGC<ZEN>TG <FAM>: Fluorophore AAGCTGGTGAC<3IABkFQ><ZEN>: Quencher <3IABkFQ>: 3′ Blocker

For detection of bacteria belonging to the species Streptococcusagalactiae (S. agalactiae), primers and probe for amplifying the gyrBgene (SEQ ID NOs: 121-123, TABLE XXII), the sip gene encoding thesurface immunogenic protein (SEQ ID NOs: 82-84, TABLE XXIII), and theddlA gene (SEQ ID NOs: 85-87, TABLE XXIV) are provided. For detection ofbacteria belonging to the Streptococcus genus, primers and probes foramplifying the tuf gene (SEQ ID NOs: 100-102, TABLE XXV) are provided.Nucleic acids other than those exemplified herein can also be used todetect Streptococcus genus-specific pathogen grouping target genes in asample. For example, functional variants can be evaluated forspecificity and/or sensitivity by those of skill in the art usingroutine methods. Representative functional variants can include, e.g.,one or more deletions, insertions, and/or substitutions in the targetgene primers and probes disclosed herein. More specifically, embodimentsof the oligonucleotides each include a nucleic acid with a sequenceselected from SEQ ID NOs: 121-123, 82-84, 85-87, 100-102 a substantiallyidentical variant thereof in which the variant has at least, e.g., 80%,90%, or 95% sequence identity to one of SEQ ID NOs: 121-123, 82-84,85-87, 100-102 or a complement of SEQ ID NOs: 121-123, 82-84, 85-87,100-102 and the variant.

TABLE XXII Oligonucleotides for detecting Streptococcus agalactiaePrimers and Probes that hybridize to gyrB gene in Streptococcus agalactiaeOligonucleotide Oligonucleotide SEQ Type Name ID NO: SequenceModifications Forward primer SEGP2921 121 ACCACTGTATTTGATTTTGATAAATTAGCCAAA Reverse primer SEGP2922 122 TTCTCATTGATAAACTCAACGTATGAACCTA Probe SEGP2923 123 <FAM>ACTAAGAAT<ZEN>CT <FAM>: FluorophoreCCATTTCAGACAAGCGAGAAG <ZEN>: Quencher GTCAAGAAGTTG<3IABkFQ><3IABkFQ>: 3′ Blocker

TABLE XXIII Oligonucleotides for detecting Streptococcus agalactiaePrimers and Probes that hybridize to sip gene in Streptococcus agalactiaeOligonucleotide Oligonucleotide SEQ ID Type Name NO: SequenceModifications Forward primer SEGP2204 82 ATCCTGAGACAACACTGACAReverse primer SEGP2205 83 TTGCTGGTGTTTCTATTTTCA Probe SEGP2206 84<CY5.5>ATCAGAAGAGT <CY5.5>: Fluorophore <BHQ_2>CATACTGCCACTTC<BHQ_2>: Quencher <Phos> <Phos>: Phosphate

TABLE XXIV Oligonucleotides for detecting Streptococcus agalactiaePrimers and Probes that hybridize to ddlA gene in Streptococcus agalactiaeOligonucleotide Oligonucleotide SEQ ID Type Name NO: SequenceModifications Forward primer SEGP2947 85 CACAAGAATTTGATGAAATGC CATCTTCAReverse primer SEGP2949 86 ACAATTGCATTATCATCATAG ATATCACTTGGA ProbeSEGP2951 87 <FAM>TAATGACAA<ZEN>ACC <FAM>: Fluorophore AAAC<ZEN>: Quencher TGTTGATTTAGACAAAATGGT <3IABkFQ>: 3′ BlockerTCGTCCA<3IABkFQ>

TABLE XXV Oligonucleotides for detecting Streptococcus GenusPrimers and Probes that hybridize to tuf gene in Streptococcus genusOligonucleotide Oligonucleotide SEQ ID Type Name NO: SequenceModifications Forward primer SEGP1705 100 GTACAGTTGCTTCAGGACGTA TCReverse primer SEGP1706 101 ACGTTCGATTTCATCACGTTG Probe SEGP1709.1 102<ATTO>TTCCGTA<BHQ_2>AA <ATTO>: Fluorophore CAACTTGACGAAGGTCTTG<ZEN>: Quencher <Phos> <Phos>: Phosphate

For detection of the common fungal pathogens: Candida albicans andCandida auris, primers and probe for amplifying the 18s ribosomal RNA(18s rRNA) gene (SEQ ID NOs: 88-90, TABLE XXVI), and the 5.8s ribosomalRNA (5.8s rRNA) gene (SEQ ID NOs: 91-93, TABLE XXVII) are provided.Nucleic acids other than those exemplified herein can also be used todetect Candida genus-specific pathogen grouping target genes in asample. For example, functional variants can be evaluated forspecificity and/or sensitivity by those of skill in the art usingroutine methods. Representative functional variants can include, e.g.,one or more deletions, insertions, and/or substitutions in the targetgene primers and probes disclosed herein. More specifically, embodimentsof the oligonucleotides each include a nucleic acid with a sequenceselected from SEQ ID NOs: 88-90, 91-93, a substantially identicalvariant thereof in which the variant has at least, e.g., 80%, 90%, or95% sequence identity to one of SEQ ID NOs: 88-90, 91-93, or acomplement of SEQ ID NOs: 88-90, 91-93 and the variant.

TABLE XXVI Oligonucleotides for detecting CandidaPrimers and Probes that hybridize to 18s rRNA gene in CandidaOligonucleotide Oligonucleotide SEQ Type Name ID NO: SequenceModifications Forward primer SEGP1712 88 CGTTTTCATTAATCAAGAA CGAAAGTTAReverse primer SEGP1713 89 ACCGATCCCTAGTCGGCAT A Probe SEGP1716 90<FAM>AGACTACGA<ZEN>C <FAM>: Fluorophore GGTATCTGATCATCTTCGA<ZEN>: Quencher TCCC<3IABkFQ> <3IABkFQ>: 3′ Blocker

TABLE XXVII Oligonucleotides for detecting CandidaPrimers and Probes that hybridize to 5.8s rRNA gene in CandidaOligonucleotide Oligonucleotide SEQ ID Type Name NO: SequenceModifications Forward primer SEGP1718 91 ACAACGGATCTCTTGGTTC TCReverse primer SEGP1719 92 GCAATGTGCGTTCAAAGA TTCGA Probe SEGP1722.1 93<FAM_Thr>TCGATGAAG<B <FAM_Thr>: HQ_2>AACGCAGCGAAATG FluorophoreCGATACG<Phos> <BHQ_2>: Quencher <Phos>: Phosphate

For detection of all types of bacteria, a primer and probe combinationfor amplifying a conserved region in the 16s ribosomal RNA (16s rRNA)gene (SEQ ID NOs: 94-96, TABLE) XVIII) is provided.

TABLE XXVIII Oligonucleotides for detecting general bacteriaPrimers and Probes that hybridize to 16s rRNA in bacteria (Gram-positiveand Gram-negative) Oligonucleotide Oligonucleotide SEQ ID Type Name NO:Sequence Modifications Forward primer SEGP1830 94 TCCTACGGGAGGCAGCAGTReverse primer SEGP1831 95 GGACTACCAGGGTATCTAATC CTGTT Probe SEGP1895.196 <CER_635>CGTATTACCGCGGC <CFR_635>: T<BHQ_2>GCTGGCAC<Phos> Fluorophore<BHQ_2>: Quencher <Phos>: Phosphate

In one embodiment, the above-described sets of primers and probes areused not only for the detection and for identification of infectiousbacteria strains but also in the performance of an antimicrobialsusceptibility testing (AST) assay. Therefore, the present inventiondiscloses methods and compositions for performing quantitative real-timePCR reactions whereby identification (ID) of bacteria and testing oftheir antimicrobial susceptibility (AST) are determined simultaneouslyat a single assay setting.

A functionally active variant of any of the primers and/or probesdisclosed herein may be identified by using the primers and/or probes inthe disclosed methods. A functionally active variant of a primer and/orprobe described herein pertains to a primer and/or probe that provide asimilar or higher specificity and sensitivity in the described method orkit as compared to the respective sequence of the primer and/or probedescribed herein.

The variant may, e.g., vary from the sequence of the primers and probesdescribed herein by one or more nucleotide additions, deletions orsubstitutions such as one or more nucleotide additions, deletions orsubstitutions at the 5′ end and/or the 3′ end of the respective sequenceof the primer and/or probe described herein. As detailed above, a primer(and/or probe) may be chemically modified, i.e., a primer and/or probemay comprise a modified nucleotide or a non-nucleotide compound. A probe(or a primer) is then a modified oligonucleotide. “Modified nucleotides”(or “nucleotide analogs”) differ from a natural “nucleotide” by somemodification but still consist of a base or base-like compound, apentofuranosyl sugar or a pentofuranosyl sugar-like compound, aphosphate portion or phosphate-like portion, or combinations thereof.For example, a “label” may be attached to the base portion of a“nucleotide” whereby a “modified nucleotide” is obtained. A natural basein a “nucleotide” may also be replaced by, e.g., a 7-deazapurine wherebya “modified nucleotide” is obtained as well. The terms “modifiednucleotide” or “nucleotide analog” are used interchangeably in thepresent application. A “modified nucleoside” (or “nucleoside analog”)differs from a natural nucleoside by some modification in the manner asoutlined above for a “modified nucleotide” (or a “nucleotide analog”).

Oligonucleotides including modified oligonucleotides and oligonucleotideanalogs that amplify a nucleic acid molecule encoding any of the targetgenes can be designed using, for example, a computer program such asOLIGO (Molecular Biology Insights Inc., Cascade, Colo.). Importantfeatures when designing oligonucleotides to be used as amplificationprimers include, but are not limited to, an appropriate sizeamplification product to facilitate detection (e.g., byelectrophoresis), similar melting temperatures for the members of a pairof primers, and the length of each primer (i.e., the primers need to belong enough to anneal with sequence-specificity and to initiatesynthesis but not so long that fidelity is reduced duringoligonucleotide synthesis). Typically, oligonucleotide primers are 8 to50 nucleotides in length (e.g., 8, 10, 12, 14, 16, 18, 20, 22, 24, 26,28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, or 50 nucleotides inlength). In some embodiments oligonucleotide primers are 40 or fewernucleotides in length.

In addition to a set of primers, the methods may use one or more probesin order to detect the presence or absence of target genes. The term“probe” refers to synthetically or biologically produced nucleic acids(DNA or RNA), which by design or selection, contain specific nucleotidesequences that allow them to hybridize under defined predeterminedstringencies specifically (i.e., preferentially) to “target nucleicacids”, in the present case to a target gene nucleic acid. A “probe” canbe referred to as a “detection probe” meaning that it detects the targetnucleic acid.

In some embodiments, the described target gene probes can be labeledwith at least one fluorescent label. In one embodiment, the target geneprobes can be labeled with a donor fluorescent moiety, e.g., afluorescent dye, and a corresponding acceptor moiety, e.g., a quencher.In one embodiment, the probe comprises or consists of a fluorescentmoiety and the nucleic acid sequences comprise or consist of the probesequences disclosed herein.

Designing oligonucleotides to be used as probes can be performed in amanner similar to the design of primers. Embodiments may use a singleprobe or a pair of probes for detection of the amplification product.Depending on the embodiment, the probe(s) use may comprise at least onelabel and/or at least one quencher moiety. As with the primers, theprobes usually have similar melting temperatures, and the length of eachprobe must be sufficient for sequence-specific hybridization to occurbut not so long that fidelity is reduced during synthesis.Oligonucleotide probes are generally 15 to 40 (e.g., 16, 18, 20, 21, 22,23, 24, or 25) nucleotides in length.

Polymerase Chain Reaction (PCR)

U.S. Pat. Nos. 4,683,202, 4,683,195, 4,800,159, and 4,965,188 discloseconventional PCR techniques. PCR typically employs two oligonucleotideprimers that bind to a selected nucleic acid template (e.g., DNA orRNA). Primers useful in some embodiments include oligonucleotidescapable of acting as points of initiation of nucleic acid synthesiswithin the described target gene nucleic acid sequences. A primer can bepurified from a restriction digest by conventional methods, or it can beproduced synthetically. The primer is preferably single-stranded formaximum efficiency in amplification, but the primer can bedouble-stranded. Double-stranded primers are first denatured, i.e.,treated to separate the strands. One method of denaturing doublestranded nucleic acids is by heating.

If the template nucleic acid is double-stranded, it is necessary toseparate the two strands before it can be used as a template in PCR.Strand separation can be accomplished by any suitable denaturing methodincluding physical, chemical or enzymatic means. One method ofseparating the nucleic acid strands involves heating the nucleic aciduntil it is predominately denatured (e.g., greater than 50%, 60%, 70%,80%, 90% or 95% denatured). The heating conditions necessary fordenaturing template nucleic acid will depend, e.g., on the buffer saltconcentration and the length and nucleotide composition of the nucleicacids being denatured, but typically range from about 90° C. to about105° C. for a time depending on features of the reaction such astemperature and the nucleic acid length. Denaturation is typicallyperformed for about 30 sec to 4 min (e.g., 1 min to 2 min 30 sec, or 1.5min).

If the double-stranded template nucleic acid is denatured by heat, thereaction mixture is allowed to cool to a temperature that promotesannealing of each primer to its target sequence on the described targetgene nucleic acid molecules. The temperature for annealing is usuallyfrom about 35° C. to about 65° C. (e.g., about 40° C. to about 60° C.;about 45° C. to about 50° C.). Annealing times can be from about 10 secto about 1 min (e.g., about 20 sec to about 50 sec; about 30 sec toabout 40 sec). The reaction mixture is then adjusted to a temperature atwhich the activity of the polymerase is promoted or optimized, i.e., atemperature sufficient for extension to occur from the annealed primerto generate products complementary to the template nucleic acid. Thetemperature should be sufficient to synthesize an extension product fromeach primer that is annealed to a nucleic acid template, but should notbe so high as to denature an extension product from its complementarytemplate (e.g., the temperature for extension generally ranges fromabout 40° C. to about 80° C. (e.g., about 50° C. to about 70° C.; about60° C.). Extension times can be from about 10 sec to about 5 min (e.g.,about 30 sec to about 4 min; about 1 min to about 3 min; about 1 min 30sec to about 2 min).

PCR assays can employ nucleic acid such as RNA or DNA (cDNA). Thetemplate nucleic acid need not be purified; it may be a minor fractionof a complex mixture, such as nucleic acid contained in human cells.Nucleic acid molecules may be extracted from a biological sample byroutine techniques such as those described in Diagnostic MolecularMicrobiology: Principles and Applications (Persing et al. (eds), 1993,American Society for Microbiology, Washington D.C.). Nucleic acids canbe obtained from any number of sources, such as plasmids, or naturalsources including bacteria, yeast, protozoa viruses, organelles, orhigher organisms such as plants or animals.

The oligonucleotide primers are combined with PCR reagents underreaction conditions that induce primer extension. For example, chainextension reactions generally include 50 mM KCl, 10 mM Tris-HCl (pH8.3), 15 mM MgCl₂, 0.001% (w/v) gelatin, 0.5-1.0 μg protodenaturedtemplate DNA, 50 pmoles of each oligonucleotide primer, 2.5 U of Taqpolymerase, and 10% DMSO). The reactions usually contain 150 to 320 μMeach of dATP, dCTP, dTTP, dGTP, or one or more analogs thereof.

The newly synthesized strands form a double-stranded molecule that canbe used in the succeeding steps of the reaction. The steps of strandseparation, annealing, and elongation can be repeated as often as neededto produce the desired quantity of amplification products correspondingto the target nucleic acid molecules. The limiting factors in thereaction are the amounts of primers, thermostable enzyme, and nucleosidetriphosphates present in the reaction. The cycling steps (i.e.,denaturation, annealing, and extension) are preferably repeated at leastonce. For use in detection, the number of cycling steps will depend,e.g., on the nature of the sample. If the sample is a complex mixture ofnucleic acids, more cycling steps will be required to amplify the targetsequence sufficient for detection. Generally, the cycling steps arerepeated at least about 20 times, but may be repeated as many as 40, 60,or even 100 times.

Fluorescence Resonance Energy Transfer (FRET)

FRET technology (see, for example, U.S. Pat. Nos. 4,996,143, 5,565,322,5,849,489, and 6,162,603) is based on a concept that when a donorfluorescent moiety and a corresponding acceptor fluorescent moiety arepositioned within a certain distance of each other, energy transfertakes place between the two fluorescent moieties that can be visualizedor otherwise detected and/or quantitated. The donor typically transfersthe energy to the acceptor when the donor is excited by light radiationwith a suitable wavelength. The acceptor typically re-emits thetransferred energy in the form of light radiation with a differentwavelength. In certain systems, non-fluorescent energy can betransferred between donor and acceptor moieties, by way of biomoleculesthat include substantially non-fluorescent donor moieties (see, forexample, U.S. Pat. No. 7,741,467).

In one example, a oligonucleotide probe can contain a donor fluorescentmoiety and a corresponding quencher, which may or not be fluorescent,and which dissipates the transferred energy in a form other than light.When the probe is intact, energy transfer typically occurs between thedonor and acceptor moieties such that fluorescent emission from thedonor fluorescent moiety is quenched the acceptor moiety. During anextension step of a polymerase chain reaction, a probe bound to anamplification product is cleaved by the 5′ to 3′ nuclease activity of,e.g., a Taq Polymerase such that the fluorescent emission of the donorfluorescent moiety is no longer quenched. Exemplary probes for thispurpose are described in, e.g., U.S. Pat. Nos. 5,210,015, 5,994,056, and6,171,785. Commonly used donor-acceptor pairs include the FAM-TAMRApair. Commonly used quenchers are DABCYL and TAMRA. Commonly used darkquenchers include BlackHole Quenchers™ (BHQ), (Biosearch Technologies,Inc., Novato, Calif.), Iowa Black™, (Integrated DNA Tech., Inc.,Coralville, Iowa), BlackBerry™ Quencher 650 (BBQ-650), (Berry & Assoc.,Dexter, Mich.).

In another example, two oligonucleotide probes, each containing afluorescent moiety, can hybridize to an amplification product atparticular positions determined by the complementarity of theoligonucleotide probes to the target nucleic acid sequence. Uponhybridization of the oligonucleotide probes to the amplification productnucleic acid at the appropriate positions, a FRET signal is generated.Hybridization temperatures can range from about 35° C. to about 65° C.for about 10 sec to about 1 min.

Fluorescent analysis can be carried out using, for example, a photoncounting epifluorescent microscope system (containing the appropriatedichroic mirror and filters for monitoring fluorescent emission at theparticular range), a photon counting photomultiplier system, or afluorimeter. Excitation to initiate energy transfer, or to allow directdetection of a fluorophore, can be carried out with an argon ion laser,a high intensity mercury (Hg) arc lamp, a fiber optic light source, orother high intensity light source appropriately filtered for excitationin the desired range.

As used herein with respect to donor and corresponding acceptor moieties“corresponding” refers to an acceptor fluorescent moiety or a darkquencher having an absorbance spectrum that overlaps the emissionspectrum of the donor fluorescent moiety. The wavelength maximum of theemission spectrum of the acceptor fluorescent moiety should be at least100 nm greater than the wavelength maximum of the excitation spectrum ofthe donor fluorescent moiety. Accordingly, efficient non-radiativeenergy transfer can be produced there between.

Fluorescent donor and corresponding acceptor moieties are generallychosen for (a) high efficiency Forster energy transfer; (b) a largefinal Stokes shift (>100 nm); (c) shift of the emission as far aspossible into the red portion of the visible spectrum (>600 nm); and (d)shift of the emission to a higher wavelength than the Raman waterfluorescent emission produced by excitation at the donor excitationwavelength. For example, a donor fluorescent moiety can be chosen thathas its excitation maximum near a laser line (for example,Helium-Cadmium 442 nm or Argon 488 nm), a high extinction coefficient, ahigh quantum yield, and a good overlap of its fluorescent emission withthe excitation spectrum of the corresponding acceptor fluorescentmoiety. A corresponding acceptor fluorescent moiety can be chosen thathas a high extinction coefficient, a high quantum yield, a good overlapof its excitation with the emission of the donor fluorescent moiety, andemission in the red part of the visible spectrum (>600 nm).

Representative donor fluorescent moieties that can be used with variousacceptor fluorescent moieties in FRET technology include fluorescein,Lucifer Yellow, B-phycoerythrin, 9-acridineisothiocyanate, LuciferYellow VS, 4-acetamido-4′-isothio-cyanatostilbene-2,2′-disulfonic acid,7-diethylamino-3-(4′-isothiocyanatophenyl)-4-methylcoumarin, succinimdyl1-pyrenebutyrate, and4-acetamido-4′-isothiocyanatostilbene-2,2′-disulfonic acid derivatives.Representative acceptor fluorescent moieties, depending upon the donorfluorescent moiety used, include LC Red 640, LC Red 705, Cy5, Cy5.5,Lissamine rhodamine B sulfonyl chloride, tetramethyl rhodamineisothiocyanate, rhodamine x isothiocyanate, erythrosine isothiocyanate,fluorescein, diethylenetriamine pentaacetate, or other chelates ofLanthanide ions (e.g., Europium, or Terbium). Donor and acceptorfluorescent moieties can be obtained, for example, from Molecular Probes(Junction City, Oreg.) or Sigma Chemical Co. (St. Louis, Mo.).

The donor and acceptor fluorescent moieties can be attached to theappropriate probe oligonucleotide via a linker arm. The length of eachlinker arm is important, as the linker arms will affect the distancebetween the donor and acceptor fluorescent moieties. The length of alinker arm can be the distance in Angstroms (Å) from the nucleotide baseto the fluorescent moiety. In general, a linker arm is from about 10 Åto about 25 Å. The linker arm may be of the kind described in WO84/03285. WO 84/03285 also discloses methods for attaching linker armsto a particular nucleotide base, and also for attaching fluorescentmoieties to a linker arm.

An acceptor fluorescent moiety, such as an LC Red 640, can be combinedwith an oligonucleotide which contains an amino linker (e.g., C6-aminophosphoramidites available from ABI (Foster City, Calif.) or GlenResearch (Sterling, Va.)) to produce, for example, LC Red 640-labeledoligonucleotide. Frequently used linkers to couple a donor fluorescentmoiety such as fluorescein to an oligonucleotide include thiourealinkers (FITC-derived, for example, fluorescein-CPG's from Glen Researchor ChemGene (Ashland, Mass.)), amide-linkers(fluorescein-NHS-ester-derived, such as CX-fluorescein-CPG from BioGenex(San Ramon, Calif.)), or 3′-amino-CPGs that require coupling of afluorescein-NHS-ester after oligonucleotide synthesis.

As described herein, amplification products can be detected usinglabeled hybridization probes that take advantage of FRET technology. OneFRET format utilizes TaqMan® technology to detect the presence orabsence of an amplification product, and hence, the presence or absenceof the target gene. TaqMan® technology utilizes one single-strandedhybridization probe labeled with, e.g., one fluorescent dye and onequencher, which may or may not be fluorescent. When a first fluorescentmoiety is excited with light of a suitable wavelength, the absorbedenergy is transferred to a second fluorescent moiety or a dark quencheraccording to the principles of FRET. The second moiety is generally aquencher molecule. During the annealing step of the PCR reaction, thelabeled hybridization probe binds to the target DNA (i.e., theamplification product) and is degraded by the 5′ to 3′ nuclease activityof, e.g., the Taq Polymerase during the subsequent elongation phase. Asa result, the fluorescent moiety and the quencher moiety becomespatially separated from one another. As a consequence, upon excitationof the first fluorescent moiety in the absence of the quencher, thefluorescence emission from the first fluorescent moiety can be detected.By way of example, an ABI PRISM® 7700 Sequence Detection System (AppliedBiosystems) uses TaqMan® technology, and is suitable for performing themethods described herein for detecting the presence or absence of thetarget gene in the sample.

Molecular beacons in conjunction with FRET can also be used to detectthe presence of an amplification product using the real-time PCRmethods. Molecular beacon technology uses a hybridization probe labeledwith a first fluorescent moiety and a second fluorescent moiety. Thesecond fluorescent moiety is generally a quencher, and the fluorescentlabels are typically located at each end of the probe. Molecular beacontechnology uses a probe oligonucleotide having sequences that permitsecondary structure formation (e.g., a hairpin). As a result ofsecondary structure formation within the probe, both fluorescentmoieties are in spatial proximity when the probe is in solution. Afterhybridization to the target nucleic acids (i.e., amplificationproducts), the secondary structure of the probe is disrupted and thefluorescent moieties become separated from one another such that afterexcitation with light of a suitable wavelength, the emission of thefirst fluorescent moiety can be detected.

Another common format of FRET technology utilizes two hybridizationprobes. Each probe can be labeled with a different fluorescent moietyand are generally designed to hybridize in close proximity to each otherin a target DNA molecule (e.g., an amplification product). A donorfluorescent moiety, for example, fluorescein, is excited at 470 nm bythe light source of the LightCycler® Instrument. During FRET, thefluorescein transfers its energy to an acceptor fluorescent moiety suchas LightCycler®-Red 640 (LC Red 640) or LightCycler®-Red 705 (LC Red705). The acceptor fluorescent moiety then emits light of a longerwavelength, which is detected by the optical detection system of theLightCycler® instrument. Efficient FRET can only take place when thefluorescent moieties are in direct local proximity and when the emissionspectrum of the donor fluorescent moiety overlaps with the absorptionspectrum of the acceptor fluorescent moiety. The intensity of theemitted signal can be correlated with the number of original target DNAmolecules (e.g., the number of target strain/family genomes). Ifamplification of target nucleic acid occurs and an amplification productis produced, the step of hybridizing results in a detectable signalbased upon FRET between the members of the pair of probes.

Generally, the presence of FRET indicates the presence of the targetgene in the sample, and the absence of FRET indicates the absence of thetarget gene in the sample. Inadequate specimen collection,transportation delays, inappropriate transportation conditions, or useof certain collection swabs (calcium alginate or aluminum shaft) are allconditions that can affect the success and/or accuracy of a test result,however. Using the methods disclosed herein, detection of FRET within,e.g., 45 cycling steps is indicative of the presence of the targetstrain/family of interest.

Representative biological samples that can be used in practicing themethods include, but are not limited to respiratory specimens, fecalspecimens, blood specimens, dermal swabs, nasal swabs, wound swabs,blood cultures, skin, and soft tissue infections. Collection and storagemethods of biological samples are known to those of skill in the art.Biological samples can be processed (e.g., by nucleic acid extractionmethods and/or kits known in the art) to release target gene nucleicacid or in some cases, the biological sample can be contacted directlywith the PCR reaction components and the appropriate oligonucleotides.

Melting curve analysis is an additional step that can be included in acycling profile. Melting curve analysis is based on the fact that DNAmelts at a characteristic temperature called the melting temperature(Tm), which is defined as the temperature at which half of the DNAduplexes have separated into single strands. The melting temperature ofa DNA depends primarily upon its nucleotide composition. Thus, DNAmolecules rich in G and C nucleotides have a higher Tm than those havingan abundance of A and T nucleotides. By detecting the temperature atwhich signal is lost, the melting temperature of probes can bedetermined. Similarly, by detecting the temperature at which signal isgenerated, the annealing temperature of probes can be determined. Themelting temperature(s) of the probes from the amplification products canconfirm the presence or absence of the target strain/family of interestin the sample.

Within each thermocycler run, control samples can be cycled as well.Positive control samples can amplify target nucleic acid controltemplate (other than described amplification products of target genes)using, for example, control primers and control probes. Positive controlsamples can also amplify, for example, a plasmid construct containingthe target nucleic acid molecules. Such a plasmid control can beamplified internally (e.g., within the sample) or in a separate samplerun side-by-side with the patients' samples using the same primers andprobe as used for detection of the intended target. Such controls areindicators of the success or failure of the amplification,hybridization, and/or FRET reaction. Each thermocycler run can alsoinclude a negative control that, for example, lacks target template DNA.Negative control can measure contamination. This ensures that the systemand reagents would not give rise to a false positive signal. Therefore,control reactions can readily determine, for example, the ability ofprimers to anneal with sequence-specificity and to initiate elongation,as well as the ability of probes to hybridize with sequence-specificityand for FRET to occur.

In an embodiment, the methods include steps to avoid contamination. Forexample, an enzymatic method utilizing uracil-DNA glycosylase isdescribed in U.S. Pat. Nos. 5,035,996, 5,683,896 and 5,945,313 to reduceor eliminate contamination between one thermocycler run and the next.

Conventional PCR methods in conjunction with FRET technology can be usedto practice the methods. In one embodiment, a LightCycler® instrument isused. The following patent applications describe real-time PCR as usedin the LightCycler® technology: WO 97/46707, WO 97/46714, and WO97/46712.

The LightCycler® can be operated using a PC workstation and can utilizea Windows NT operating system. Signals from the samples are obtained asthe machine positions the capillaries sequentially over the opticalunit. The software can display the fluorescence signals in real-timeimmediately after each measurement. Fluorescent acquisition time is10-100 milliseconds (msec). After each cycling step, a quantitativedisplay of fluorescence vs. cycle number can be continually updated forall samples. The data generated can be stored for further analysis.

As an alternative to FRET, an amplification product can be detectedusing a double-stranded DNA binding dye such as a fluorescent DNAbinding dye (e.g., SYBR® Green or SYBR® Gold (Molecular Probes)). Uponinteraction with the double-stranded nucleic acid, such fluorescent DNAbinding dyes emit a fluorescence signal after excitation with light at asuitable wavelength. A double-stranded DNA binding dye such as a nucleicacid intercalating dye also can be used. When double-stranded DNAbinding dyes are used, a melting curve analysis is usually performed forconfirmation of the presence of the amplification product.

It is understood that the embodiments of the present disclosure are notlimited by the configuration of one or more commercially availableinstruments.

Real-Time PCR for Phenotypic Antimicrobial Susceptibility Testing (AST)

Although quantitative real-time PCR (qPCR or qRT-PCR) can identify andquantify bacteria in samples with high specificity and sensitivity, itsreliability in performing phenotypic based AST using growth of bacteriain the presence of antimicrobials has not been demonstrated withconsistency. The present invention utilizes mathematical relationshipsderived from PCR growth curves to make the determination of whether atested bacteria strain is susceptible, intermediate or resistant (SIR)to a given antimicrobial. The principle behind a phenotypic AST testusing PCR is depicted in FIG. 1. In the absence of antimicrobial (shownas Reference), bacteria have ongoing genomic DNA replication. In thepresence of an antimicrobial, resistant bacteria will replicate withsimilar number of genome copies as the Reference, while susceptiblebacteria will experience inhibition of replication resulting in fewercopies. This difference in growth provides a phenotypic readout that canbe determined by qPCR.

Raw data from a hypothetical qPCR experiment in which either a resistantor a susceptible bacteria strain is incubated for four hours withvarious concentrations of an antimicrobial shown in FIG. 2. In FIG. 2A,the raw qPCR data is depicted as growth curves where fluorescence (e.g.from a TaqMan probe) is measured at each PCR cycle. For the resistantisolate, the growth curve appears similar irrespective of incubation forfour hours at different antimicrobial concentrations, whereas in thesusceptible isolate, a dose-dependent decrease in fluorescent intensityand increase in the number of cycles required for the signal to crossbackground (threshold) level, which is commonly referred as the Cyclethreshold or Ct value. In FIG. 2B the same qPCR data is representedbased on the Ct value, where a resistant isolate has little or no changein Ct value as a function of antimicrobial concentration, while asusceptible isolate has a dose dependent increase in Ct value bydetecting a smaller number of replicating bacteria.

qPCR data can be used to determine whether a strain is susceptible,intermediate or resistant to a given antimicrobial by exploring avariety of mathematical relationships that are shown on FIG. 3. FIG. 3Adescribes mathematical relationships such as “Slope”, “Ct”,“Inflection”, “Absolute Fluorescence Intensity (AFI)”, and “EndpointRelative Intensity (ERI)” describe the behavior of the raw qPCRamplification curve. As shown in FIG. 3B, these features can further beevaluated as a function of antimicrobial exposure by relating numericalvalues obtained in the presence of antimicrobial back to the numericalvalues obtained in the absence of the antimicrobial. Relative changes inthese features, such as □Ct or □AFI can then be used to determine strainMIC to a given drug allowing strain resistance and susceptibilitydetermination utilizing approved breakpoints.

From the calculated differences in the mathematical features, simplifiedpartitioning models such as that depicted in FIG. 4 were used toclassify bacteria isolates as resistant or susceptible. Partitioningutilizes the Gini Index to determine which feature and thresholdmaximizes dispersion of the two classes. Only two splits are utilized toprevent overfitting and allows for graphical representation in twodimensions for easy visualization.

EXAMPLES

The following examples, tables and figures are provided to aid theunderstanding of the subject matter, the true scope of which is setforth in the appended claims. It is understood that modifications can bemade in the procedures set forth without departing from the spirit ofthe invention.

Example 1 PCR Conditions

Real-time PCR detection of target genes were performed using the Cobas®6800/8800 systems platforms (Roche Molecular Systems, Inc., Pleasanton,Calif.). The final concentrations of the amplification reagents areshown below:

TABLE XXIX PCR Amplification Reagents Master Mix Component Final Cone(45.0 uL) DMSO 5.4 % NaN3 0.027 % Potassium acetate 120.0 mM Glycerol3.0 % Tween 20 0.015 % NaN3 0.027 % Tricine 60.0 mM NTQ21-46AAptamer0.222 uM UNG Enzyme 10.0 U Z05D-DNA Polymerase 45.0 U dATP 400.0 uM dCTP400.0 uM dGTP 400.0 uM dUTP 800.0 uM Forward primer oligonucleotides0.50 μM Reverse primer oligonucleotides 0.50 μM Probe oligonucleotides0.15 μM Manganese Acetate 3.30 mM Trizma Base 12 μM Methylparaben 0.08 %

The following table shows the typical thermoprofile used for PCRamplification reaction:

TABLE XXX PCR Thermoprofile Program Name Target (° C.) Acquisition ModeHold (hh:mm:ss) Ramp Rate (° C./s) Cycles Analysis Mode Pre-PCR 50 None00:02:00 4.4 1 None 94 None 00:00:05 4.4 55 None 00:02:00 2.2 60 None00:06:00 4.4 65 None 00:04:00 4.4 1st Measurement 95 None 00:00:05 4.4 5Quantification 55 Single 00:00:30 2.2 2nd Measurment 91 None 00:00:054.4 45 Quantification 58 Single 00:00:25 2.2 Cooling 40 None 00:02:002.2 1 None

The Pre-PCR program comprised initial denaturing and incubation at 55°C., 60° C. and 65° C. for reverse transcription of RNA templates.Incubating at three temperatures combines the advantageous effects thatat lower temperatures slightly mismatched target sequences (such asgenetic variants of an organism) are also transcribed, while at highertemperatures the formation of RNA secondary structures is suppressed,thus leading to a more efficient transcription. PCR cycling was dividedinto two measurements, wherein both measurements apply a one-step setup(combining annealing and extension). The first 5 cycles at 55° C. allowfor an increased inclusivity by pre-amplifying slightly mismatchedtarget sequences, whereas the 45 cycles of the second measurementprovide for an increased specificity by using an annealing/extensiontemperature of 58° C.

Example 2 PCR Using Primers/Probes for Detecting Enterobacterales Order

Using the PCR conditions described in Example 1, PCR assays usingforward primer RM_ENTF (SEQ ID NO: 1), reverse primer RM_ENTRP (SEQ IDNO: 2) and both probes RM_ETP02 (SEQ ID NO: 3) and RM_ETP02B (SEQ ID NO:4) that target the rplP gene were tested against five bacteria strainsfrom the Enterobacterales order: E. Coli, K pneumonia, E. cloacae, S.marcescens, P. mirabilis, and two bacteria strains fromnon-Enterobacterales order: P. aeruginosa, and A. baumannii. Theconcentration of the starting material that used ranged between 1e8 and5e8 CFU/ml for the culture fluid for all the strains (overnight culturespreviously stored in glycerol) except for S. marcescens in which DNA(˜1e7 copies/up was used. No sample preparation was performed for theculture fluids. The results of this experiment showed that growth curvesare observed only for the five strains of the Enterobacterales orderfamily but not for the two non-Enterobacterales strains, therebydemonstrating good inclusivity and exclusivity profiles for thisparticular combination of primers and probes for detectingEnterobacterales. Similar experiments were performed testing the P.aeruginosa-specific primers and probe (SEQ ID NOs: 130-133) and the A.baumannii-specific primers and probe (SEQ ID NOs: 17-19) which alsoshowed good specificity and exclusivity (data not shown).

PCR assays using forward primer SEGP1899 (SEQ ID NO: 8), reverse primerSEGP1901 (SEQ ID NO: 9) and probe SEGP2016 (SEQ ID NO: 10) that targetthe gyrB gene were tested against common Gram-negative pathogens: E.coli, K pneumoniae, E. cloacae, K oxytoca, K. aerogenes, S. marcescens,P. mirabilis, S. maltophilia, P. aeruginosa, A. baumannii, and A.pittii. Gram-positive organisms were also tested and showed nomeaningful amplification (data not shown). The concentration of thegenomic DNA was roughly 2-10 ng/uL for all samples, besides the notemplate control that was 0 ng/uL. As shown in FIG. 5, growth curveswere observed only for the species that constitute the orderEnterobacterales (including E. coli, K. pneumoniae, E. cloacae, Koxytoca, K aerogenes, S. marcescens, and P. mirabilis). No meaningfulamplification was observed for non-target organisms (S. maltophilia, P.aeruginosa, A. baumannii, and A. pittii), thereby demonstrating goodinclusivity and exclusivity profiles for this particular combination ofprimers and probes for detecting Enterobacterales.

PCR assays were performed for other primers and probe combinationsdesigned to target the rplP gene in Enterobacterales. PCR assays usingforward primer SEGP2891 (SEQ ID NO: 5), reverse primer SEGP2892 (SEQ IDNO: 6) and probe SEGP2893 (SEQ ID NO: 7) that target the rplP gene weretested against common Gram-negative pathogens: E. coli, K pneumoniae, E.cloacae, K. oxytoca, K. aerogenes, S. marcescens, P. mirabilis, S.maltophilia, P. aeruginosa, A. baumannii, and A. pittii. Gram-positiveorganisms were also tested and showed no meaningful amplification (datanot shown). The concentration of the genomic DNA was roughly 2-10 ng/uLfor all samples, besides the no template control which was 0 ng/uL. Asshown in FIG. 6, growth curves were observed only for the species thatconstitute the order Enterobacterales (including E. coli, K. pneumoniae,E. cloacae, K. oxytoca, K aerogenes, S. marcescens, and P. mirabilis).No meaningful amplification was observed for non-target organisms (S.maltophilia, P. aeruginosa, A. baumannii, and A. pittii), therebydemonstrating good inclusivity and exclusivity profiles for thisparticular combination of primers and probes for detectingEnterobacterales.

Similar results were obtained in PCR assays using forward primerSEGP2799 (SEQ ID NO: 11), reverse primers SEGP2800 (SEQ ID NO: 12),SEGP2802 (SEQ ID NO: 13), and SEGP2821 (SEQ ID NO: 14), in combinationwith probes SEGP2804 (SEQ ID NO: 15) and SEGP2822 (SEQ ID NO: 16) thattarget the rpoB gene. As shown in FIG. 7, growth curves were observedonly for the species that constitute the order Enterobacterales(including E. coli, K pneumoniae, E. cloacae, K. oxytoca, K aerogenes,S. marcescens, and P. mirabilis). No meaningful amplification wasobserved for non-target organisms (S. maltophilia, P. aeruginosa, A.baumannii, and A. pittii), thereby demonstrating good inclusivity andexclusivity profiles for this particular combination of primers andprobes for detecting Enterobacterales.

Example 3 PCR Using Primers/Probes for Detecting Acinetobacter Genus

PCR assays using forward primer SEGP2603 (SEQ ID NO: 20), reverse primerSEGP2606 (SEQ ID NO: 21), and probe SEGP2769 (SEQ ID NO: 22) that targetthe ompA gene were tested against common Gram-negative pathogens: E.coli, K pneumoniae, E. cloacae, K. oxytoca, K aerogenes, S. marcescens,P. mirabilis, S. maltophilia, P. aeruginosa, A. baumannii, and A.pittii. Gram-positive organisms were also tested and showed nomeaningful amplification (data not shown). The concentration of thegenomic DNA was roughly 2-10 ng/uL for all samples, besides the notemplate control that was 0 ng/uL. As shown in FIG. 8, growth curveswere observed only for the prevalent pathogens that are within the genusAcinetobacter (A. baumannii and A. pittii). No meaningful amplificationwas observed for non-target organisms (E. coli, K pneumoniae, E.cloacae, K oxytoca, K. aerogenes, S. marcescens, P. mirabilis, S.maltophilia, and P. aeruginosa), thereby demonstrating good inclusivityand exclusivity profiles for this particular combination of primers andprobes for detecting Acinetobacter.

Similar results were obtained in PCR assays using forward primerSEGP2590 (SEQ ID NO: 23), reverse primer SEGP2593 (SEQ ID NO: 24), andprobe SEGP2594 (SEQ ID NO: 25) that target the rpoB gene (as shown inFIG. 9), and in PCR assays using forward primer SEGP2626 (SEQ ID NO:26), reverse primer SEGP2628 (SEQ ID NO: 27) and probe SEGP2629 (SEQ IDNO: 28) that target the gyrB gene (as shown in FIG. 10). Theseexperiments demonstrate good inclusivity and exclusivity profiles forboth combinations of primers and probes for detecting Acinetobacter.

Example 4 PCR Using Primers/Probes for Detecting Pseudomonas aeruginosa

PCR assays using forward primer SEGP2341 (SEQ ID NO: 32), reverse primerSEGP2342 (SEQ ID NO: 33) and probe SEGP2343 (SEQ ID NO: 34) that targetthe tuf gene were tested against common Gram-negative pathogens: E.coli, K pneumoniae, E. cloacae, K oxytoca, K. aerogenes, S. marcescens,P. mirabilis, S. maltophilia, P. aeruginosa, A. baumannii, and A.pittii. Gram-positive organisms were also tested and showed nomeaningful amplification (data not shown). The concentration of thegenomic DNA was roughly 2-10 ng/uL for all samples, besides the notemplate control that was 0 ng/uL. As shown in FIG. 11, growth curveswere observed only for pathogens within the genus Pseudomonas (P.aeruginosa). No meaningful amplification was observed for non-targetorganisms (E. coli, K pneumoniae, E. cloacae, K oxytoca, K. aerogenes,S. marcescens, P. mirabilis, S. maltophilia, A. baumannii, and A.pittii), thereby demonstrating good inclusivity and exclusivity profilesfor this particular combination of primers and probes for detecting P.aeruginosa.

Similar results were obtained in PCR assays using forward primerSEGP2630 (SEQ ID NO: 35), reverse primer SEGP2631 (SEQ ID NO: 36), andprobe SEGP2632 (SEQ ID NO: 37) that target the gyrB gene (as shown inFIG. 12), and in PCR assays using forward primer SEGP2634 (SEQ ID NO:38), reverse primer SEGP2637 (SEQ ID NO: 39) and probe SEGP2640 (SEQ IDNO: 40) that target the rpoB gene (as shown in FIG. 13). Theseexperiments demonstrate good inclusivity and exclusivity profiles forboth combinations of primers and probes for detecting P. aeruginosa.

Example 5 PCR Using Primers/Probes for Detecting Stenotrophomonasmaltophilia

PCR assays using forward primer SEGP2532 (SEQ ID NO: 41), reverse primerSEGP2538 (SEQ ID NO: 42) and probe SEGP2544 (SEQ ID NO: 43) that targetthe fdnG gene were tested against common Gram-negative pathogens: E.coli, K pneumoniae, E. cloacae, K. oxytoca, K. aerogenes, S. marcescens,P. mirabilis, S. maltophilia, P. aeruginosa, A. baumannii, and A.pittii. Gram-positive organisms were also tested and showed nomeaningful amplification (data not shown). The concentration of thegenomic DNA was roughly 2-10 ng/uL for all samples, besides the notemplate control that was 0 ng/uL. As shown in FIG. 14, growth curveswere observed only for the species of Stenotrophomonas maltophilia (S.maltophilia). No meaningful amplification was observed for non-targetorganisms (E. coli, K pneumoniae, E. cloacae, K oxytoca, K. aerogenes,S. marcescens, P. mirabilis, P. aeruginosa, A. baumannii, and A.pittii), thereby demonstrating good inclusivity and exclusivity profilesfor this particular combination of primers and probes for detecting S.maltophilia.

Similar results were obtained in PCR assays using forward primerSEGP2578 (SEQ ID NO: 44), reverse primer SEGP2579 (SEQ ID NO: 45), andprobe SEGP2580 (SEQ ID NO: 46) that target the gyrB gene (as shown inFIG. 15), and in PCR assays using forward primer SEGP2572 (SEQ ID NO:47), reverse primer SEGP2573 (SEQ ID NO: 48) and probe SEGP2574 (SEQ IDNO: 49) that target the tuf gene (as shown in FIG. 16). Theseexperiments demonstrate good inclusivity and exclusivity profiles forboth combinations of primers and probes for detecting S. maltophilia.

Example 6 PCR Using Primers/Probes for Detecting Enterococcus Genus

PCR assays using forward primer SEGP2522 (SEQ ID NO: 53), reverse primerSEGP2525 (SEQ ID NO: 54), and probe SEGP2770 (SEQ ID NO: 55) that targetthe rpoB gene were tested against common Gram-positive pathogens: S.agalactiae, S. pneumoniae, S. pyogenes, E. faecium, E. faecalis, S.aureus, and S. epidermidis. Gram-negative organisms were also tested andshowed no meaningful amplification (data not shown). The concentrationof the genomic DNA was roughly 2-10 ng/uL for all samples, besides theno template control that was 0 ng/uL. As shown in FIG. 17, amplificationcurves are observed only for pathogens within the genus Enterococcus (E.faecium and E. faecalis). No meaningful amplification was observed fornon-target organisms (S. agalactiae, S. pneumoniae, S. pyogenes, S.aureus, and S. epidermidis), thereby demonstrating good inclusivity andexclusivity profiles for this particular combination of primers andprobes for detecting Enterococcus.

Similar results were obtained in PCR assays using forward primersSEGP1624 (SEQ ID NO: 56) and SEGP1627 (SEQ ID NO: 57), reverse primersSEGP1625 (SEQ ID NO: 58) and SEGP1628 (SEQ ID NO: 59), and probesSEGP1626 (SEQ ID NO: 60) and SEGP1629 (SEQ ID NO: 61) that target theddl gene (as shown in FIG. 18). Good specificity was also observed inPCR assays using forward primers SEGP2882 (SEQ ID NO: 62) and SEGP2884(SEQ ID NO: 63), reverse primers SEGP2885 (SEQ ID NO: 64) and SEGP2886(SEQ ID NO: 65) and probe SEGP2888 (SEQ ID NO: 66) that target the gyrBgene (as shown in FIG. 19). These experiments demonstrate goodinclusivity and exclusivity profiles for both combinations of primersand probes for detecting Enterococcus.

Example 7 PCR Using Primers/Probes for Detecting Staphylococcus aureus

PCR assays using forward primer SEGP1490 (SEQ ID NO: 67), reverse primerSEGP1491 (SEQ ID NO: 68) and probe SEGP1492 (SEQ ID NO: 72) that targetthe CPE gene were tested against common Gram-positive pathogens: S.agalactiae, S. pneumoniae, S. pyogenes, E. faecium, E. faecalis, S.aureus, and S. epidermidis. Gram-negative organisms were also tested andshowed no meaningful amplification (data not shown). The concentrationof the genomic DNA was roughly 2-10 ng/uL for all samples, besides theno template control that was 0 ng/uL. As shown in FIG. 20, meaningfulgrowth curves were observed only for pathogens within the speciesStaphylococcus aureus. No meaningful amplification was observed fornon-target organisms (S. agalactiae, S. pneumoniae, S. pyogenes, E.faecium, E. faecalis, and S. epidermidis), thereby demonstrating goodinclusivity and exclusivity profiles for this particular combination ofprimers and probes for detecting S. aureus.

Similar results were obtained in PCR assays using forward primerSEGP2792 (SEQ ID NO: 73), reverse primer SEGP2793 (SEQ ID NO: 74), andprobe SEGP2794 (SEQ ID NO: 75) that target the gyrB gene (as shown inFIG. 21), and in PCR assays using forward primer SEGP2932 (SEQ ID NO:76), reverse primer SEGP2933 (SEQ ID NO: 77) and probe SEGP2935 (SEQ IDNO: 78) that target the ddlA gene (as shown in FIG. 22). Theseexperiments demonstrate good inclusivity and exclusivity profiles forboth combinations of primers and probes for detecting S. aureus.

Example 8 PCR Using Primers/Probes for Detecting Streptococcusagalactiae

PCR assays using forward primer SEGP2921 (SEQ ID NO: 121), reverseprimer SEGP2922 (SEQ ID NO: 122) and probe SEGP2923 (SEQ ID NO: 123)that target the gyrB gene were tested against common Gram-positivepathogens: S. agalactiae, S. pneumoniae, S. pyogenes, E. faecium, E.faecalis, S. aureus, and S. epidermidis. Gram-negative organisms werealso tested and showed no meaningful amplification (data not shown). Theconcentration of the genomic DNA was roughly 2-10 ng/uL for all samples,besides the no template control that was 0 ng/uL. As shown on FIG. 23,meaningful growth curves were observed only for pathogens within thespecies Streptococcus agalactiae. No meaningful amplification wasobserved for non-target organisms (S. pneumoniae, S. pyogenes, E.faecium, E. faecalis, S. aureus, and S. epidermidis), therebydemonstrating good inclusivity and exclusivity profiles for thisparticular combination of primers and probes for detecting S.agalactiae.

Similar results were obtained in PCR assays using forward primerSEGP2204 (SEQ ID NO: 82), reverse primer SEGP2205 (SEQ ID NO: 83), andprobe SEGP2206 (SEQ ID NO: 84) that target the sip gene (as shown inFIG. 24), and in PCR assays using forward primer SEGP2947 (SEQ ID NO:85), reverse primer SEGP2949 (SEQ ID NO: 86) and probe SEGP2951 (SEQ IDNO: 87) that target the ddlA gene (as shown in FIG. 25). Theseexperiments demonstrate good inclusivity and exclusivity profiles forboth combinations of primers and probes for detecting S. agalactiae.

Example 9 PCR Using Primers/Probes for Detecting Candida Genus

PCR assays using forward primer SEGP1712 (SEQ ID NO: 88), reverse primerSEGP1713 (SEQ ID NO: 89), and probe SEGP1716 (SEQ ID NO: 90) that targetthe RDN18 (18s rRNA) were tested against common fungal pathogens:Candida albicans and Candida auris. Gram-negative and positive organismswere also tested and showed no meaningful amplification (data notshown). The concentration of the genomic DNA was roughly 2-10 ng/uL forall samples, besides the no template control that was 0 ng/uL. As shownin FIG. 26, meaningful amplification curves were observed only forpathogens within the genus Candida. No meaningful amplification wasobserved for non-target organisms, thereby demonstrating goodinclusivity and exclusivity profiles for this particular combination ofprimers and probes for detecting Candida.

PCR assays using forward primer SEGP1718 (SEQ ID NO: 91), reverse primerSEGP1719 (SEQ ID NO: 92), and probe SEGP1722.1 (SEQ ID NO: 93) thattarget the RDN58 (5.8s rRNA) gene were tested against C. albicans and C.auris. Gram-negative and positive organisms were also tested and showedno meaningful amplification (data not shown). The concentration of thegenomic DNA was roughly 2-10 ng/uL for all samples, besides the notemplate control that was 0 ng/uL. As shown in FIG. 27, meaningfulamplification curves were observed only for pathogens within the genusCandida. No meaningful amplification was observed for non-targetorganisms, thereby demonstrating good inclusivity and exclusivityprofiles for this particular combination of primers and probes fordetecting Candida.

Example 10 PCR for Detecting Common Gram-Negative and Gram-PositivePathogens

PCR assays using forward primer SEGP1830 (SEQ ID NO: 94), reverse primerSEGP1831 (SEQ ID NO: 95) and probe SEGP1895.1 (SEQ ID NO: 96) thattarget the 16s gene were tested against common Gram-negative pathogens:E. coli, K pneumoniae, E. cloacae, K. oxytoca, K aerogenes, S.marcescens, P. mirabilis, S. maltophilia, P. aeruginosa, A. baumannii,and A. pittii. The concentration of the genomic DNA was roughly 2-10ng/uL for all samples, besides the no template control that was 0 ng/uL.As shown on FIG. 28, amplification curves were observed for allGram-negative pathogens, thereby demonstrating this particularcombination of primers and probes for the detection of commonGram-negative pathogens.

This same combination of primers and probe that target the 16s gene wasalso tested against common Gram-positive pathogens: S. agalactiae, S.pneumoniae, S. pyogenes, E. faecium, E. faecalis, S. aureus, and S.epidermidis under identical concentrations. As shown on FIG. 29,amplification curves were observed for all Gram-positive pathogens,thereby demonstrating this particular combination of primers and probesfor the detection of common Gram-positive pathogens.

Example 11 Interpretation of AST Results

In general, the two most commonly used guidelines for interpretingAntimicrobial Susceptibility Testing (AST) results are guidelines fromthe: 1) Clinical Laboratory Standards Institute (CLSI), and 2) EuropeanCommittee on Antimicrobial Susceptibility Testing (EUCAST). The US usesthe CLSI guidelines while the European countries use the EUCASTguidelines. The current version from CLSI is M100 ED30, “PerformanceStandards for Antimicrobial Susceptibility Testing, 30th Edition”, andavailable via URL:clsi.org/standards/products/microbiology/documents/m100. The currentversion from EUCAST is Version 10, “The European Committee onAntimicrobial Susceptibility Testing. Breakpoint tables forinterpretation of MICs and zone diameters. Version 10.0, 2020” andavailable via URL:www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0Breakpoint_Tables.pdf.

In FIGS. 30-1 and 30-2, the established Minimum Inhibitory Concentration(MIC) breakpoints indicated as □g/mL for a number of Gram-negativebacterial organisms (Enterobacterales order, P. aeruginosa,Acinetobacter genus, S. maltophilia) as determined by the Clinical andLaboratory Standards Institute (CLSI) document M100 ED 30. Breakpointsare used to interpret MIC results from Antimicrobial SusceptibilityTesting, and to classify “groupings” of organisms as either Susceptible,Intermediate, or Resistant (SIR) to a given antimicrobial. Groupings oforganisms can be at differing levels, including, but not limited to,species, genus, order, or a specific biochemical property.

In FIG. 31, the established Minimum Inhibitory Concentration (MIC)breakpoints indicated as □g/mL for a number of Gram-positive bacterialorganisms (S. aureus and S. lugdunensis, S. epidermidis, Enterococcusgenus, S. pneumonia, Streptococcus/□-hemolytic, Viridans Streptococcus)as determined by the Clinical and Laboratory Standards Institute (CLSI)document M100 ED 30. Breakpoints are used to interpret MIC results fromAntimicrobial Susceptibility Testing, and to classify “groupings” oforganisms as either Susceptible, Intermediate, or Resistant (SIR) to agiven antimicrobial. Groupings of organisms can be at differing levels,including, but not limited to, species, genus, order, or a specificbiochemical property.

In FIG. 32, the established Minimum Inhibitory Concentration (MIC)breakpoints indicated as □g/mL for fungal organisms (Candida albicans,Candida glabrata, Candida krusei, Candida tropicalis, Candida auris) asdetermined by the Clinical and Laboratory Standards Institute (CLSI)document M60 ED 1. Breakpoints are used to interpret MIC results fromAntifungal Susceptibility Testing (AFST), and to classify “groupings” oforganisms as either Susceptible, Intermediate, or Resistant (SIR) to agiven antifungal. Groupings of organisms can be at differing levels,including, but not limited to, species, genus, order, or a specificbiochemical property. Of note is that while AFST is recommended forCandida auris, neither CLSI or CDC currently have establishedbreakpoints for the species; instead, AFST results from closely relatedCandida spp. and expert opinion are used to determine the susceptibilityof C. auris isolates to a given antifungal.

Example 12 PCR ID/AST Assay Protocol Methods and Materials:

-   a. Prepare antimicrobial (Abx) Plate ahead of time and store at−80 C    until needed    -   i. Diluent—Cation Adjusted Mueller Hinton Broth (CAMHB)    -   ii. Final Vol—50 ul/well    -   iii. Remove from −80 C and let thaw at 30 min/Room Temp prior to        use

TABLE XXXI Antimicrobial (Abx) Plate Layout Antibiotic (Abx) PlateLayout 1 2 3 4 S 6 7 8 9 10 11 12 A 0 Abx 1/4 Abx 1/2 Abx 1 Abx 2 Abx 4Abx 0 Abx 1/4 Abx 1/2 Abx 1 Abx 2 Abx 4 Abx B 0 Abx 1/4 Abx 1/2 Abx 1Abx 2 Abx 4 Abx 0 Abx 1/4 Abx 1/2 Abx 1 Abx 2 Abx 4 Abx C 0 Abx 1/4 Abx1/2 Abx 1 Abx 2 Abx 4 Abx 0 Abx 1/4 Abx 1/2 Abx 1 Abx 2 Abx 4 Abx D 0Abx 1/4 Abx 1/2 Abx 1 Abx 2 Abx 4 Abx 0 Abx 1/4 Abx 1/2 Abx 1 Abx 2 Abx4 Abx E 0 Abx 1/4 Abx 1/2 Abx 1 Abx 2 Abx 4 Abx 0 Abx 1/4 Abx 1/2 Abx 1Abx 2 Abx 4 Abx F 0 Abx 1/4 Abx 1/2 Abx 1 Abx 2 Abx 4 Abx 0 Abx 1/4 Abx1/2 Abx 1 Abx 2 Abx 4 Abx G 0 Abx 1/4 Abx 1/2 Abx 1 Abx 2 Abx 4 Abx 0Abx 1/4 Abx 1/2 Abx 1 Abx 2 Abx 4 Abx H 0 Abx 1/4 Abx 1/2 Abx 1 Abx 2Abx 4 Abx 0 Abx 1/4 Abx 1/2 Abx 1 Abx 2 Abx 4 Abx

-   b. Overnight cultures in CAMHB—37 C/16-18 hrs/500 rpm    -   i. 10 ul glycerol stock+490 ul CAMHB in 2 mL 96-well Deep Well        Plate-   c. Normalize cultures to 1.00E+06 CFU/mL by Optical Density (OD)-   d. Prepare Test Plate by adding 50 ul normalized test isolate to    appropriate wells of Abx Plate as outlined

TABLE XXXII Test Isolate Layout on Abx Plate Test isolate Layout onAntibiotic (Abx) Plate 1 2 3 4 5 6 7 8 9 10 11 12 A Isolate_1 Isolate_9 B Isolate_2 Isolate_10 C Isolate_3 Isolate_11 D Isolate_4 Isolate_12 EIsolate_5 Isolate_13 F Isolate_6 Isolate_14 G Isolate_7 Isolate_15 HIsolate_8 Isolate_16

-   e. Incubate Test Plate at 37 C/4 hrs/no shaking-   f. Prepare PCR Reagents according to TABLE XXIX-   g. Add 45 ul Master Mix to each well of a PCR Assay Plate-   h. Following incubation, stamp 5 ul/well of Test Plate to PCR Assay    Plate-   i. Final Vol—50 ul/well-   i. For Test Plate, continue incubating at 37 C/12-16 hrs/no shaking    to determine reference method Minimum Inhibitory Concentration (MIC)-   j. Load PCR Assay Plate to cobas z 480 instrument and run under    conditions of TABLE XXX.-   k. Following incubation read Test Plate for MIC and determine    phenotypic Susceptible/Intermediate/Resistant interpretation.

Example 13 Real-Time PCR ID and AST Assay of Enterobacterales Order

Rapid identification and phenotypic antimicrobial susceptibility testingof Enterobacterales utilizing three distinct target genes, gyrB, rplP,and rpoB, and three classes of antibacterial agents ciprofloxacin(fluoroquinolone), gentamicin (aminoglycoside), and meropenem(carbapenem) was performed. The primer/probe sets used were as follows.For gyrB, SEQ ID NO: 8 (forward primer), SEQ ID NO: 9 (reverse primer),SEQ ID NO: 10 (probe); for rplP, SEQ ID NO: 5 (forward primer), SEQ IDNO: 6 (reverse primer), SEQ ID NO: 7 (probe); for rpoB, SEQ ID NO: 11(forward primer), SEQ ID NOs: 12-14 (reverse primers), SEQ ID NOs: 15-16(probe). The antimicrobial susceptibility of K. pneumoniae strains 0143(antimicrobial resistant strain) and 16565 (antimicrobial sensitivestrain) were interpreted according to the Clinical and LaboratoryStandards Institute (CLSI) document M100 ED 30 to determine theirresistance and susceptibility to the given antimicrobials, respectively.Each strain was inoculated at 5E5 CFU/mL into wells containing variousconcentrations of the indicated antimicrobials, and after 4 h ofincubation were subjected to PCR-based rapid ID/AST testing using theprotocol of Example 12.

The results are shown on FIG. 33. The percentages on the Y-axis depictedas “Fold Change Abx level 1” were determined using the calculation2{circumflex over ( )}-(Abx_Level_1_Ct−Reference_Ct) or 2{circumflexover ( )}-(□Ct). The Abx Level indication does not relate to an actualconcentration that was used but is rather an indication of which 2-folddilution is being referred to where Abx Level 1 is the lowestconcentration and each Level up is 2-fold higher concentration (seeTABLE XXXI). To give an example of how Fold Change is calculated, if theReference_Ct value (i.e. the Ct value with no antimicrobial added) is 20and the Abx_Level_1_Ct value is 22, then the Fold Change=2{circumflexover ( )}−(22-20)=2{circumflex over ( )}−2=½×½=25%. Based on thesecalculations, strains resistant to the antimicrobial which have lower□Ct values will have higher “Fold Change” values than strains that aresensitive to the antimicrobial which have higher □Ct values, and in FIG.33, Abx_Level_1 was able to produce the best separation between theresistant strain Kpn 0143 and the sensitive strain Kpn 16565. These datafurther indicate that all three gene targets (gyrB, rplB, rpoB) can beutilized to obtain correct susceptibility results for both Kpn strains,in determining sensitivity or resistance to ciprofloxacin, gentamicin,and meropenem. However, there may be instances in which any given targetgene may perform better or worse for determining sensitivity orresistance to a given antimicrobial. Taken together, these resultsindicate that different target genes and alleles can be utilized forrapid PCR-based ID/AST of the Enterobacterales Order as long as theprimers and probes can exhibit correct inclusivity and exclusivitycriteria for Enterobacterales as was shown in Example 2, FIGS. 5-7.

Example 14 Real-Time PCR ID and AST Assay of Pseudomonas aeruginosa

Rapid Identification and phenotypic antimicrobial susceptibility testingof Pseudomonas aeruginosa utilizing three distinct target genes, tuf,gyrB, rpoB, and three classes of antibacterial agents, ciprofloxacin,gentamicin, and meropenem, was performed. The primer/probe sets usedwere as follows. For tuf, SEQ ID NO: 32 (forward primer), SEQ ID NO: 33(reverse primer), SEQ ID NO: 34 (probe); for gyrB, SEQ ID NO: 35(forward primer), SEQ ID NO: 36 (reverse primer), SEQ ID NO: 37 (probe);for rpoB, SEQ ID NO: 38 (forward primer), SEQ ID NO: 39 (reverseprimer), SEQ ID NO: 40 (probe). The antimicrobial susceptibility of P.aeruginosa strains 16657 (resistant) and 17816 (sensitive) wereinterpreted according to the Clinical and Laboratory Standards Institute(CLSI) document M100 ED 30 to determine their resistance andsusceptibility to the given antimicrobials, respectively. Each strainwas inoculated at 5E5 CFU/mL into wells containing variousconcentrations of the indicated antimicrobials, and after 4 h ofincubation were subjected to PCR-based rapid ID/AST testing using theprotocol of Example 12. The results, as shown in FIG. 34, indicate thatall three gene targets can be utilized to obtain correct susceptibilityresults for both P. aeruginosa strains, though some target alleles doseem to perform better for some antimicrobials. Taken together, theseresults indicate that different target genes and alleles can be utilizedfor rapid PCR-based ID/AST given they provide the correct inclusivityand exclusivity criteria for P. aeruginosa (see FIGS. 11-13).

Example 15 Real-Time PCR ID and AST Assay of Acinetobacter baumanii

Rapid Identification and phenotypic antimicrobial susceptibility testingof Acinetobacter baumanii utilizing three distinct target genes, ompA,rpoB, gyrB, and three classes of antibacterial agents, ciprofloxacin,gentamicin, and meropenem, was performed. The primer/probe sets usedwere as follows. For ompA, SEQ ID NO: 20 (forward primer), SEQ ID NO: 21(reverse primer), SEQ ID NO: 22 (probe); for rpoB, SEQ ID NO: 23(forward primer), SEQ ID NO: 24 (reverse primer), SEQ ID NO: 25 (probe);for gyrB, SEQ ID NO: 26 (forward primer), SEQ ID NO: 27 (reverseprimer), SEQ ID NO: 28 (probe). The antimicrobial susceptibility of A.baumannii strains 17694 (resistant) and 16421 (sensitive) wereinterpreted according to the Clinical and Laboratory Standards Institute(CLSI) document M100 ED 30 to determine their resistance andsusceptibility to the given antimicrobials, respectively. Each strainwas inoculated at 5E5 CFU/mL into wells containing variousconcentrations of the indicated antimicrobials, and after 4 h ofincubation were subjected to PCR-based rapid ID/AST testing using theprotocol of Example 12. The results, as shown in FIG. 35, indicate thatall three gene targets can be utilized to obtain correct susceptibilityresults for both Abi strains, though some target alleles do seem toperform better for some antimicrobials. Taken together, these resultsindicate that different target genes and alleles can be utilized forrapid PCR-based ID/AST given they provide the correct inclusivity andexclusivity criteria for A. baumannii (see FIGS. 8-10).

Example 16 Real-Time PCR ID and AST Assay of Staphylococcus aureus

Rapid Identification and phenotypic antimicrobial susceptibility testingof Staphylococcus aureus utilizing three distinct target genes (gyrB,ddlA, tuf) and one class of antibacterial agent, cefoxitin(cephalosporin) was performed. The primer/probe sets used were asfollows. For gyrB, SEQ ID NO: 73 (forward primer), SEQ ID NO: 74(reverse primer), SEQ ID NO: 75 (probe); for ddlA, SEQ ID NO: 76(forward primer), SEQ ID NO: 77 (reverse primer), SEQ ID NO: 78 (probe);for tuf SEQ ID NO: 79 (forward primer), SEQ ID NO: 80 (reverse primer),SEQ ID NO: 81 (probe). The antimicrobial susceptibility of S. aureusstrains 15509 (resistant) and 16405 (sensitive) were interpretedaccording to the Clinical and Laboratory Standards Institute (CLSI)document M100 ED 30 to determine their resistance and susceptibility tothe given antimicrobials, respectively. Each strain was inoculated at5E5 CFU/mL into wells containing various concentrations of the indicatedantimicrobial, and after 4 h of incubation were subjected to PCR-basedrapid ID/AST testing using the protocol of Example 12. The results, asshown in FIG. 36, indicate that all three gene targets can be utilizedto obtain correct susceptibility results for both S. aureus strains,though some target alleles do seem to perform better. Taken together,these results indicate that different target genes and alleles can beutilized for rapid PCR-based ID/AST given they provide the correctinclusivity and exclusivity criteria for S. aureus (see FIGS. 21-22).

Example 17 Real-Time PCR ID and AST Assay of Enterococcus faecium

Rapid Identification and phenotypic antimicrobial susceptibility testingof Enterococcus faecium utilizing three distinct target genes (rpoB,ddl, gyrB) and two classes of antibacterial agents, ampicillin(beta-lactam) and vancomycin (glycopeptide) was performed. Theprimer/probe sets used were as follows. For rpoB, SEQ ID NO: 53 (forwardprimer), SEQ ID NO: 54 (reverse primer), SEQ ID NO: 55 (probe); for ddl,SEQ ID NOs: 56-57 (forward primers), SEQ ID NOs: 58-59 (reverseprimers), SEQ ID NOs: 60-61 (probes); for gyrB, SEQ ID NOs: 62-63(forward primers), SEQ ID NOs: 64-65 (reverse primers), SEQ ID NO: 66(probe). The antimicrobial susceptibility of E. faecium strains 18483(resistant) and 18446 (sensitive) were interpreted according to theClinical and Laboratory Standards Institute (CLSI) document M100 ED 30to determine their resistance and susceptibility to the givenantimicrobials, respectively. Each strain was inoculated at 5E5 CFU/mLinto wells containing various concentrations of the indicatedantimicrobial, and after 4 h of incubation were subjected to PCR-basedrapid ID/AST testing using the protocol of Example 12. The results, asshown in FIG. 37, indicate that all three gene targets can be utilizedto obtain correct susceptibility results for both E. faecium strains,though some target alleles do seem to perform better. Taken together,these results indicate that different target genes and alleles can beutilized for rapid PCR-based ID/AST given they provide the correctinclusivity and exclusivity criteria for E. faecium (see FIGS. 17-19).

Example 18 Real-Time PCR ID and AST Assay of Candida Genus

Rapid Identification and phenotypic antimicrobial susceptibility testingof Candida can be performed with the target genes RDN18 (18s ribosomalRNA) and RDN58 (5.8s ribosomal RNA) using the primers and probes asshown in FIG. 38 which are for RDN18: SEQ ID NO: 88 (forward primer),SEQ ID NO: 89 (reverse primer), SEQ ID NO: 90 (probe); and for RDN58:SEQ ID NO: 91 (forward primer), SEQ ID NO: 92 (reverse primer), SEQ IDNO: 93 (probe). The correct inclusivity and exclusivity criteria forCandida are shown in FIGS. 26-27.

Example 19 Generic Real-Time PCR ID and AST Assay

Rapid Identification and phenotypic antimicrobial susceptibility testingof any given Gram-negative or Gram-positive bacteria can be performedwith the widely conserved 16s ribosomal RNA gene as target and using theprimers and probe as shown in FIG. 39, which are SEQ ID NO: 94 (forwardprimer), SEQ ID NO: 95 (reverse primer), and SEQ ID NO: 96 (probe).

Example 20 Multiplex PCR ID Assay with Breakpoint Groups

FIG. 40A shows the inclusivity and exclusivity performance of aGram-negative pathogen PCR multiplex master mix. The Acinetobacter PCRdetection set utilized forward primer SEGP2603 (SEQ ID NO: 20), reverseprimer SEGP2606 (SEQ ID NO: 21) and probe SEGP2769 (SEQ ID NO: 22) thattargets the ompA gene (see TABLE V) and assay results are reported inchannel 1. The Pseudomonas aeruginosa PCR detection set utilized forwardprimer SEGP2341 (SEQ ID NO: 32), reverse primer SEGP2342 (SEQ ID NO: 33)and probe SEGP2343 (SEQ ID NO: 34) that targets the tuf gene (see TABLEVIII) and assay results are reported in channel 2. The EnterobacteralesPCR detection set utilized forward primer SEGP1899 (SEQ ID NO: 8),reverse primer SEGP1901 (SEQ ID NO: 9) and probe SEGP2016 (SEQ ID NO:10) and targets the gyrB gene (see TABLE III) and assay results arereported in channel 3. General bacterial PCR detection set utilizedforward primer SEGP1830 (SEQ ID NO: 94), reverse primer SEGP1831 (SEQ IDNO: 95) and probe SEGP1895.1 (SEQ ID NO: 96) targets the 16s rRNA gene(see TABLE XXVIII) and assay results are reported in channel 4. Lastly,a generic internal control PCR detection set utilized forward primerSEGP1952 (ACAACCGCGCCATACATGTCAAGA<t_BB_dC>; SEQ ID NO: 97), reverseprimer SEGP1953 (GTCGGGCCGCTTATACAGTACCA<t_BB_dC>; SEQ ID NO: 98) andprobe SEGP1954 (<CY5.5>TGCGCGTCCCG<BHQ 2>TTTTGATACTTCGTAACGGTGC<Phos>;SEQ ID NO: 99) and assay results are reported in channel 5. Thebreakpoint groups, channels, and dye wavelengths are summarized in FIG.40B. The concentration of the genomic DNA was roughly 2-10 ng/uL for allsamples. The multiplex reaction was tested against genomic DNA isolatedfrom common Gram-negative pathogens: E. coli, K pneumoniae, E. cloacae,K. oxytoca, K. aerogenes, S. marcescens, P. mirabilis, S. maltophilia,P. aeruginosa, A. baumannii, and A. pittii. Additionally, no meaningfulamplification was observed with genomic DNA isolated from commonGram-positive pathogens (data not shown). As designed, amplificationcurves are observed in the correct channel for desired pathogens,indicating the multiplex reaction has very strong inclusivity andexclusivity.

FIG. 41A shows the inclusivity and exclusivity performance of aGram-positive pathogen PCR multiplex master mix. The Streptococcus PCRdetection set utilized forward primer SEGP1705 (SEQ ID NO: 100), reverseprimer SEGP1706 (SEQ ID NO: 101) and probe SEGP1709.1 (SEQ ID NO: 102)that targets the tuf gene (see TABLE XXV) and assay results are reportedin channel 1. The Staphylococcus PCR detection set utilized forwardprimer SEGP1835 (SEQ ID NO: 79), reverse primer SEGP1836 (SEQ ID NO: 80)and probe SEGP1838 (SEQ ID NO: 81) that targets the tuf gene (see TABLEXXI) and assay results are reported in channel 2. The Enterococcus PCRdetection set utilized forward primer SEGP2522 (SEQ ID NO: 53), reverseprimer SEGP2525 (SEQ ID NO: 54) and probe SEGP2770 (SEQ ID NO: 55) thattargets the rpoB gene (see TABLE XV) and assay results are reported inchannel 3. General bacterial PCR detection set utilized forward primerSEGP1830 (SEQ ID NO: 94), reverse primer SEGP1831 (SEQ ID NO: 95) andprobe SEGP1895.1 (SEQ ID NO: 96) that targets the 16s rRNA gene (seeTABLE)(XVIII) and assay results are reported in channel 4. Lastly, ageneric internal control PCR detection set utilized forward primerSEGP1952 (SEQ ID NO: 97), reverse primer SEGP1953 (SEQ ID NO: 98) andprobe SEGP1954 (SEQ ID NO: 99) and assay results are reported in channel5. The breakpoint groups, channels, and dye wavelengths are summarizedin FIG. 41B. The concentration of the genomic DNA was roughly 2-10 ng/uLfor all samples. The multiplex reaction was tested against purifiedgenomic DNA from common Gram-positive pathogens: S. agalactiae, S.pneumoniae, S. pyogenes, E. faecium, E. faecalis, S. aureus, and S.epidermidis. Additionally, no meaningful amplification was observed withgenomic DNA isolated from common Gram-negative pathogens (data notshown). As designed, amplification curves are observed in the correctchannel for desired pathogens, indicating the multiplex reaction hasvery strong inclusivity and exclusivity.

Example 21 Analysis of PCR-AST Assay

FIG. 42 contains graphs from a series of PCR-AST assays on diverseGram-negative strains showing different thresholds that can be used todistinguish between susceptible and resistant isolates of multiplepathogen groups separated into different channels and interpreted usingstatistical separation of populations as outlined in FIG. 4. Thethresholds associated with ciprofloxacin susceptibility are shown for A)Acinetobacter baumannii (Abi) using primers/probe of SEQ ID NOs: 17-19that target the ompA gene, B) Enterobacteriaceae (Entero) usingprimers/probe of SEQ ID NOs: 1-3 that target the rplP gene, and C)Pseudomonas aeruginosa (Pae) using primers/probe as shown in TABLEXXXIII and target the 0-antigen acetylase gene, and are based on changein Ct value at 2 ug/mL ciprofloxacin relative to no ciprofloxacincontrol (□Ct), Relative Fluorescence Intensity (RFI) at 0.5 ug/mLciprofloxacin and □Ct at 1 ug/mL ciprofloxacin, and Slope prior to theCt fluorescence value at 0.5 ug/mL ciprofloxacin (Slope) and □Ct at 1ug/mL ciprofloxacin.

TABLE XXXIII Oligonucleotides for detecting Pseudomonas aeruginosaPrimers and Probes that hybridize to O-antigen acetylase gene in P. aeruginosaOligonucleotide Oligonucleotide SEQ ID Type Name NO: SequenceModifications Forward primer RM_PFP01 130 ACGTTTTCCCTTCGCTG<t_BB_t_BB_dA = dA> t-butylbenzyl-dA Reverse primer RM_PRP02 131GTACAGTGACCAGCCAT<t_BB_ t_BB_dC = 1 dC> t-butylbenzyl-dC Reverse primerRM_PRP04 132 GCGAAACAATCCAGGCCAT<t_ t_BB_dC = 2 BB_dC> t-butylbenzyl-dCProbe RM_P04 133 <FAM_Thr>CCTAGG<BHQ_2>T <FAM_Thr>:GAATGCGCTGTTCGATGCGTT Fluorophore GGC<Phos> <BHQ_2>: Quencher<Phos>: Phosphate

FIG. 43A) shows the distribution of the resistant and susceptibleisolates that were tested for Abi, Pae, and for the Enterobacteriaceaefamily subdivided into the strains E. cloacae (Ed), E. Coli (Eco), K.aerogenes (Kae), and K. pneumonia (Kpn). The sensitivity, specificity,and categorical agreement for ciprofloxacin across species using thethresholds in FIG. 42 are shown in FIG. 43B). Sensitivity is defined asTotal Positives/(Total Positives+False Negatives); Specificity isdefined as Total Negatives/(Total Negatives+False Positives);Categorical Agreement is defined as (Total Positives+TotalNegatives)/(Total Positives+False Negatives+Total Negatives+FalsePositives).

FIG. 44 contains graphs from a second PCR-AST assay where thresholdsassociated with gentamicin susceptibility are shown for A) Abi, B)Entero, and C) Pae, using the respective primers/probe sets, and arebased on Inflection cycle at 1 ug/mL gentamicin, changes in AbsoluteFluorescence Intensity (□AFI) at 1 ug/mL gentamicin and 8 ug/mLgentamicin, and Goodness of Fit for the curve fit to the rawfluorescence data at 16 ug/mL gentamcin and □AFI at 4 ug/mL gentamicin.FIG. 45A) shows the distribution of the resistant and susceptibleisolates that were tested for Abi, Pae, and for the Enterobacteriaceaestrains Enterobacter cloacae (Ed), Escherichia coli (Eco), Klebsiellaaerogenes (Kae) and Klebsiella pneumonia (Kpn). The sensitivity,specificity and categorical agreement for gentamicin across speciesusing the thresholds in FIG. 44 are seen in FIG. 45B).

FIG. 46 contains graphs from a third PCR-AST assay where thresholdsassociated with meropenem susceptibility are shown for A) Abi, B)Entero, and C) Pae, using the respective primers/probe sets, and arebased on change in Ct value at 4 ug/mL meropenem relative to nomeropenem control (□Ct), change in Ct value at 4 ug/mL meropenemrelative to the lowest meropenem concentration at 0.25 ug/mL (□Abx-Ct)and the absolute Ct value (Ct) at 0.25 ug/mL meropenem, and the AbsoluteFluorescence Intensity (AFI) at 1 ug/mL meropenem and □Ct at 4 ug/mLmeropenem. FIG. 47A) shows the distribution of the resistant andsusceptible isolates that were tested for Abi, Pae, and for theEnterobacteriaceae strains Ed, Eco, Kae and Kpn. The sensitivity,specificity and categorical agreement for gentamicin across speciesusing the thresholds in FIG. 46 are seen in FIG. 47B).

FIG. 48A) describes the workflow for testing bacteria isolates directlyfrom positive blood culture samples, which were created by spiking afixed concentration of bacteria into whole blood, separating red bloodcells, inoculating plasma containing bacteria into a commercial bloodculture bottle, incubating overnight, and then following the PCR-ASTassay protocol as described in EXAMPLE 12 for testing isolates known forbeing resistant or susceptible to gentamicin. FIG. 48B) shows theresults of this experiment where the change in Ct value (□Ct) are usedto distinguish between resistant and susceptible isolates, showing thatphenotypic results can be obtained on bacteria directly from positiveblood culture.

Example 22 Multiplex ID-AST PCR Assay of Polymicrobial Samples

A. Kpn/Abi Multiplex PCR ID-AST assay was performed in a polymicrobialsample where a 1:1 ratio of two Gram-negative organisms, Klebsiellapneumonia (Kpn) and Acinetobacter baumannii (Abi) with differentsusceptibility combinations were co-incubated together in the absence orpresence of three different antibiotics, ciproflaxocin, gentamicin andmeropenem, at varying concentrations. Detection of the Kpn signal wasfrom an ATTO-labeled probe and detection of the Abi signal was from aHEX-labeled probe. Primers and probes used in this assay are shown inTABLE XXXIV and the results are shown on FIG. 49. Each species displayedthe appropriate phenotype in the corresponding detection channel asindicated by a delta-Ct threshold that separates susceptible (sensitive)and resistant strains, thereby providing accurate antimicrobialsusceptibility results for this polymicrobial situation.

TABLE XXXIV Oligonucleotides Used in Kpn and Abi ID-AST AssayPrimers and Probes used in polymicrobial ID-AST assay with Klebsiella pneumoniaeand Acinetobacter baumannii Oligonucleotide Oligonucleotide SEQ ID TypeName NO: Sequence Modifications Forward primers SEGP1899  8TGTCGAATTCTTATGACTCCTCCAG SEGP1813 TA 29 ACCCTAACGCTACTGCACGTReverse primers SEGP1901  9 CGCGAGCGCTTCGTCGA SEGP1815 30GGTTGATCCCAAGCGAAACCT Probes SEGP2016 10 <HEX>CCGGTCTGC<ZEN>ACCACA<HEX>: Fluorophore TGGTATTCGAGGTGG<3IABkFQ> <ATTO>: Fluorophore SEGP195131 <ATTO>TCGAAGGT<BHQ_2>CACAC <ZEN>: Quencher AGATAACACT<Phos><BHQ_2>: Quencher <3IABkFQ>: 3′ Blocker <Phos>: 3′ BlockerB. Kpn/Sar Multiplex PCR ID-AST assay was performed in a polymicrobialsample where a 1:1 ratio of one Gram-negative organism Klebsiellapneumonia (Kpn) and one Gram-positive organism Staphylococcus aureus(Sar) with different susceptibility combinations were co-incubatedtogether in the absence or presence of three different antibiotics,ciprofloxacin, cefoxitin and meropenem, at varying concentrations.Detection of the Kpn signal was from a HEX-labeled probe and detectionof the Sar signal was from a FAM-labeled probe. Primers and probes usedin this assay are shown in TABLE XXXV and the results are shown on FIG.50. N/A indicates that there is no clinically relevant interpretationfor the corresponding bacteria-drug combination. Each species displayedthe appropriate phenotype in the corresponding detection channel asindicated by a delta-Ct threshold that separates susceptible (sensitive)and resistant strains, thereby providing accurate antimicrobialsusceptibility results for this polymicrobial situation.

TABLE XXXV Oligonucleotides Used in Kpn and Sar ID-AST AssayPrimers and Probes used in polymicrobial ID-AST assay with Klebsiella pneumoniaeand Staphylococcus aureus Oligonucleotide Oligonucleotide SEQ Type NameID NO: Sequence Modifications Forward SEGP1899  8TGTCGAATTCTTATGACTCCTCCAGTA primers SEGP1835 79CCGTGTTGAACGTGGTCAAATCAAA Reverse primers SEGP1901  9 CGCGAGCGCTTCGTCGASEGP1836 80 AGCAGCTAATACTTGACCACGTTGTA Probes SEGP2016 10<HEX>CCGGTCTGC<ZEN>ACCACATG <HEX>: Fluorophore GTATTCGAGGTGG<3IABkFQ><FAM>: Fluorophore SEGP1838 81 <FAM>AGACTACGC<ZEN>TGAAGCTG<ZEN>: Quencher GTGAC<3IABkFQ> <3IABkFQ>: 3′ BlockerC. Kpn/Cal Multiplex PCR ID-AST assay was performed in a polymicrobialsample where a 1:1 ratio of one Gram-negative organism, Klebsiellapneumonia (Kpn), and one fungal organism, Candida albicans (Cal) withdifferent susceptibility combinations were co-incubated together in theabsence or presence of two different antibiotics, ciprofloxacin andmeropenem, at varying concentrations. Detection of the Kpn signal wasfrom a HEX-labeled probe and detection of the Cal signal was from aFAM-labeled probe. Primers and probes used in this assay are shown inTABLE XXXVI and the results are shown on FIG. 51. N/A indicates thatthere is no clinically relevant interpretation for the correspondingorganism-drug combination. Cal susceptibility for fluconazole isindicated. The Kpn strains displayed the appropriate phenotype in thecorresponding detection channel as indicated by a delta-Ct thresholdthat separates susceptible and resistant isolates, providing accurateantimicrobial susceptibility results.

TABLE XXXVI Oligonucleotides Used in Kpn and Cal ID-AST AssayPrimers and Probes used in polymicrobial ID-AST assay with Klebsiella pneumoniaeand Candida albicans Oligonucleotide Oligonucleotide SEQ ID Type NameNO: Sequence Modifications Forward primers SEGP1899  8TGTCGAATTCTTATGACTCCTCCA GTA SEGP1712 88 CGTTTTCATTAATCAAGAACGAAA GTTAReverse primers SEGP1901  9 CGCGAGCGCTTCGTCGA SEGP1713 89ACCGATCCCTAGTCGGCATA Probes SEGP2016 10 <HEX>CCGGTCTGC<ZEN>ACCAC<HEX>: Fluorophore ATGGTATTCGAGGTGG<3IABkFQ> <FAM>: Fluorophore SEGP171690 <FAM>AGACTACGA<ZEN>CGGTA <ZEN>: Quencher TCTGATCATCTTCGATCCC<3IABkFQ>: 3′ <3IABkFQ> BlockerD. Efs/Sar Multiplex PCR ID-AST assay was performed in a polymicrobialsample where a 1:1 ratio of two Gram-positive organisms, Enterococcusfaecalis (Efs) and Staphylococcus aureus (Sar), with differentsusceptibility combinations were co-incubated together in the absence orpresence of vancomycin at varying concentrations. Detection of the Efssignal was from a HEX-labeled probe and detection of the Sar signal wasfrom a FAM-labeled probe. Primers and probes used in this assay areshown in TABLE XXXVII and the results are shown on FIG. 52. Both speciesdisplayed the appropriate phenotype in the corresponding detectionchannel as indicated by a delta-Ct threshold that separates susceptibleand resistant isolates, providing accurate antimicrobial susceptibilityresults for this polymicrobial situation.

TABLE XXXVII Oligonucleotides Used in Efs and Sar ID-AST AssayPrimers and Probes used in polymicrobial ID-AST assay with Enterococcusfaecalis and Staphylococcus aureus Oligonucleotide OligonucleotideSEQ ID Type Name NO: Sequence Modifications Forward SEGP1624 56CGTAGCATTCTATGATTATGAAGCC primers SEGP1835 79 CCGTGTTGAACGTGGTCAAATCAAAReverse primers SEGP1625 58 CATCGTGTAAGCTAACTTCG SEGP1836 80AGCAGCTAATACTTGACCACGTTGTA Probes SEGP1626 60<HEX>CAGATTCCA<ZEN>GCCGAAGT <HEX>: SEGP1838 GCC<3IABkFQ> Fluorophore 81<FAM>AGACTACGC<ZEN>TGAAGCT <FAM>: GGTGAC<3IABkFQ> Fluorophore<ZEN>: Quencher <3IABkFQ>: 3′ BlockerE. Sar/Cal Multiplex PCR ID-AST assay was performed in a polymicrobialsample where a 1:1 ratio of one Gram-positive organism, Staphylococcusaureus (Sar) and one fungal organism Candida albicans (Cal), withdifferent susceptibility combinations were co-incubated together in theabsence or presence of cefoxitin at varying concentrations. Detection ofthe Sar signal was from a FAM-labeled probe and detection of the Calsignal was from a HEX-labeled probe. Primers and probes used in thisassay are shown in TABLE XXXVIII and the results are shown on FIG. 53.N/A indicates that there is no clinically relevant interpretation forthe corresponding organism-drug combination. Cal susceptibility forfluconazole is indicated. The Sar strains displayed the appropriatephenotype in the corresponding detection channel as indicated by adelta-Ct threshold that separates susceptible and resistant isolates,providing accurate antimicrobial susceptibility results.

TABLE XXXVIII Oligonucleotides Used in Sar and Cal ID-AST AssayPrimers and Probes used in polymicrobial ID-AST assay with Staphylococcusaureus and Candida albicans Oligonucleotide Oligonucleotide SEQ ID TypeName NO: Sequence Modifications Forward SEGP1835 79CCGTGTTGAACGTGGTCAAATC primers AAA SEGP1712 88 CGTTTTCATTAATCAAGAACGAAAGTTA Reverse primers SEGP1836 80 AGCAGCTAATACTTGACCACGTT GTA SEGP171389 ACCGATCCCTAGTCGGCATA Probes SEGP1838 81 <FAM>AGACTACGC<ZEN>TGAA<HEX>: Fluorophore SEGP1717 GCTGGTGAC<3IABkFQ> <FAM>: Fluorophore 134<HEX>AGACTACGA<ZEN>CGGT <ZEN>: Quencher ATCTGATCATCTTCGATCCC<3IABkFQ>: 3′ Blocker <3IABkFQ>

Example 23 PCR Assays for Determining Mechanism of Carbapenem Resistance

PCR assays that target the blaKPC, blaVIM, blaNDM, and blaOXA-48 geneswere tested against Gram-negative pathogens with known mechanisms ofcarbapenem resistance: K. pneumoniae, E. cloacae, P. aeruginosa, A.baumannii, E. coli and K. aerogenes. The primers and probes used in thisassay are listed in TABLE XXXIX. The concentration of the genomic DNAwas roughly 2-10 ng/□L for all samples other than the no templatecontrol. The results of the experiment are shown on FIG. 54. Growthcurves, depicted as Positive (Pos) in the figure were observed only forthe targeted resistance mechanism. No meaningful amplification wasobserved for non-target resistance mechanisms, thereby demonstratinggood inclusivity and exclusivity profiles for this particularcombination of primers and probes for detecting common mechanisms ofcarbapenem resistance.

TABLE XXXIX Oligonucleotides Used in Carbapenem Resistance PCR AssayGene Oligonucleotide Oligonucleotide SEQ ID Target Type Name NO:Sequence Modifications blaKPC Forward Primer SEGP2124 103GCGATACCACGTTCCGT CTG blaVIM SEGP2135 104 CCGAGTGGTGAGTATCC GAC blaNDMSEGP2127 105 TTTGGCGATCTGGTTTT CCG blaOXA-48 SEGP2133 106GGCACGTATGAGCAAG ATGC blaKPC Reverse Primer SEGP2125 107CGGTCGTGTTTCCCTTT AGC blaVIM SEGP2136 108 GAATGCGTGGGAATCTC GTTC blaNDMSEGP2128 109 ATCAAACCGTTGGAAGC GAG blaOXA-48 SEGP2134 110GTTTGACAATACGCTGG CTGC blaKPC Probe SEGP2126 111 <CFR_635>AGCGGCAGC<CFR_635>: AGTTT<BHQ_2>GTTGAT Fluorophore TG<Phos> <BHQ_2>: blaVIMSEGP2137 112 <CFR_635>CGCTGTATC Quencher AATCAA<BHQ_2>AAGC <Phos>: 3′AACTCATCA<Phos> Blocker blaNDM SEGP2129 113 <CFR_635>AGACATTCGGTGCGA<BHQ_2>GCTG GC<Phos> blaOXA-48 SEGP2346 114 <CFR_635>TCGGGCAATGT<BHQ_2>AGACAGTT TCTGGCTCGACG<Phos>

Example 24 Species-Specific PCR ID-AST Assays

PCR assays using forward primer SEGP2164 (SEQ ID NO: 115), reverseprimer SEGP2166 (SEQ ID NO: 116) and probe SEGP2167 (SEQ ID NO: 117)that target the citC gene of P. stuartii, and also forward primerSEGP2119 (SEQ ID NO: 118), reverse primer SEGP2121 (SEQ ID NO: 119) andprobe SEGP2120 (SEQ ID NO: 120) that target the invA gene of Salmonellawere tested against common Gram-negative pathogens: E. coli, Kpneumoniae, E. cloacae, K. oxytoca, K. aerogenes, S. marcescens, P.mirabilis, C. freundii, P. stuartii, P. rettgeri, S. enterica, S.maltophilia, P. aeruginosa, A. baumannii, and A. pittii. The sequencesare shown in TABLE XL. Gram-positive organisms were also tested andshowed no meaningful amplification (data not shown). The concentrationof the genomic DNA was roughly 2-10 ng/uL for all samples, besides theno template control which was 0 ng/uL. As shown in FIG. 55, meaningfulamplification curves were species-specific. No meaningful amplificationwas observed for non-target organisms, thereby demonstrating goodinclusivity and exclusivity profiles for the four combinations ofprimers and probes for detecting the respective Gram-negative targetspecies. These results represent non-limiting examples of speciesspecific detection sets that allow improved breakpoint based AST callingfor some specific species within the order Enterobacterales. CLSIguidelines indicate that some Enterobacterales species such as thoseshown here are resistant to specific aminoglycoside drugs, while themajority of Enterobacterales species are not.

TABLE XL Oligonucleotides for detecting P. stuartii and SalmonellaPrimers and Probes targeting citC gene of P. Stuartii and invA geneof Salmonella Oligonucleotide Oligonucleotide SEQ ID Type Name NO:Sequence Modifications Forward primer SEGP2164 115GCCATCGTGATGAATGCCAATCC SEGP2119 118 TGACCATTTCAATGGGAACTCTGCReverse primer SEGP2166 116 TCAGAGCCTTTGTGGATAGTGAGA SEGP2121 119AGATCGCCAATCAGTCCTAACGA Probe SEGP2167 117 <FAM>TTGGCTACA<ZEN>TTTATT<FAM>: TGTCGTCAAAGAAGATACCTCACG Fluorophore CTTCC<3IABkFQ><ZEN>: Quencher SEGP2120 120 <FAM>CAAAGGCGA<ZEN>GCAGC <3IABkFQ>: 3′CGCTCAGTATTGAGGA<3IABkFQ> Blocker

PCR assays using forward primer SEGP2921 (SEQ ID NO: 121), reverseprimer SEGP2922 (SEQ ID NO: 122) and probe SEGP2923 (SEQ ID NO: 123)that target the gyrB gene of S. agalactiae, forward primer SEGP2947 (SEQID NO: 85), reverse primer SEGP2949 (SEQ ID NO: 86) and probe SEGP2951(SEQ ID NO: 87) that target the ddlA gene of S. agalactiae, forwardprimer SEGP2777 (SEQ ID NO: 124), reverse primer SEGP2778 (SEQ ID NO:125) and probe SEGP2779 (SEQ ID NO: 126) that target the tuf gene of S.pneumoniae and forward primer SEGP2113 (SEQ ID NO: 127), reverse primerSEGP2114 (SEQ ID NO: 128) and probe SEGP2115 (SEQ ID NO: 129) thattarget the speB gene of S. pyogenes were tested against commonGram-positive pathogens: S. agalactiae, S. pneumoniae, S. pyogenes, E.faecium, E. faecalis, S. aureus, and S. epidermidis. The sequences areshown in TABLE XLI. Gram-negative organisms were also tested and showedno meaningful amplification (data not shown). The concentration of thegenomic DNA was roughly 2-10 ng/uL for all samples, besides the notemplate control which was 0 ng/uL. As shown in FIG. 56, meaningfulamplification curves were species-specific. No meaningful amplificationwas observed for non-target organisms, thereby demonstrating goodinclusivity and exclusivity profiles for the four combinations ofprimers and probes for detecting the respective Gram-positive targetspecies. These results represent non-limiting examples ofspecies-specific detection sets that allow improved breakpoint based ASTcalling for some specific species within the Staphylococcus andStreptococcus genera (see CLSI breakpoint tables in FIG. 31), by havingthese ID-wells a more general ID/AST detection set such as those shownin FIG. 41 can be utilized.

TABLE XLIOligonucleotides for detecting S. agalactiae, S. pneumoniae and S. pyogenesPrimers and Probes targeting gyrB gene of S. agalactiae, ddlA gene ofS. agalactiae, tuf gene of S. pneumonia, speB gene of S. pyogenesOligonucleotide Oligonucleotide SEQ ID Type Name NO: SequenceModifications Forward SEGP2921 121 ACCACTGTATTTGATTTTGATAAATTAGCCAAAprimer SEGP2947  85 CACAAGAATTTGATGAAATGCCATCTTCA SEGP2777 124GTGACTCTAAATACGAAGACATCGTT SEGP2113 127 CGGAAGAAGCCGTCAGAGACReverse primer SEGP2922 122 TTCTCATTGATAAACTCAACGTATGAACCTA SEGP2949  86ACAATTGCATTATCATCATAGATATCACTTGGA SEGP2778 125 GCAATGGTTTGTCAGTGTCACGSEGP2114 128 ATGGTGCTGACGGACGTAAC Probe SEGP2923 123<FAM>ACTAAGAAT<ZEN>CTCCATTTCAGACA <FAM>: AGCGAGAAGGTCAAGAAGTTG<3IABkFQ>Fluorophore SEGP2951  87 <FAM>TAATGACAA<ZEN>ACCAAACTGTTGAT <ZEN>:TTAGACAAAATGGTTCGTCCA<3IABkFQ> Quencher SEGP2779 126<FAM>TGAACACAG<ZEN>TTGATGAGTATATC <3IABkFQ>: CCA<3IABkFQ> 3′ BlockerSEGP2115 129 <FAM>CACCCCAAC<ZEN>CCCAGTTAACA <3IABkFQ>

The impact of using species-specific primer/probe sets in makingaccurate calls in PCR ID-AST assays can be seen in FIG. 57. In the leftpanel, use of non-species-specific primers and probes may result in theinability to discriminate between susceptible and resistant strains. Incontrast, in the right panel, the use of species-specific primer/probesets that provide identification enables separate interpretation foreach individual species, leading to improved Categorial Agreement to theCLSI breakpoint guidelines.

Example 25 Interpretation of PCR ID-AST Assay Data

FIG. 58 depicts a workflow of a PCR ID-AST assay data interpretationstrategy wherein a sigmoidal function is fit to the raw PCR curve datafollowed by calculation of curve parameters and features. Features arethen compared between the presence of various antibiotic concentrationsand the no-antibiotic reference to derive relative feature changes.Regression modeling of feature values and changes across antibioticlevels are also used to generate additional features that correspond tothe feature dose-response relationship, and may include the use ofOrdinary Least Squares, Ridge Regression, Lasso, Elastic Net, BayesianRegression, or Logistic Regression models. Features are then assembledinto a dataframe and are input into separate machine learning algorithmsalong with the ground truth MIC, or ground truth S/I/R, in order totrain predictive models, which may include Neural Networks, Tree-BasedModels, Support Vector Machine, or Nearest-Neighbor classifiers.Training consists of splitting the data into a training set and ahold-out test set, followed by splitting the training set into k-foldswith crossvalidation to search the appropriate hyperparameter space foreach type of classifier. Models are then selected based on averagecrossvalidation scores as well as performance on the held-out test set.Trained models then participate as an ensemble to return the finalpredicted MIC, which can be based on unweighted voting, weighted voting,average probabilities, weighted probabilities, or interpreted by adownstream classifier of the aforementioned classifier types.

FIG. 59 shows a diagram indicating how Species ID, AntimicrobialSusceptibility Testing, Resistance Mechanism detection, and Universal16s rRNA phenotypic information is combined to return a result, whereinSpecies ID is used to select the appropriate algorithm for MICprediction which is then compared to the appropriate breakpoints fromregulatory bodies to determine susceptibility information. Detection ofa resistance mechanism associated with the antibiotic that was testedcan then influence the susceptibility result that is returned dependingon whether its presence is consistent with the predicted MIC. In theabsence of a Species ID, the 16s rRNA phenotypic information can be usedto return a generic MIC with no susceptibility result, which can be usedin conjunction with a Species ID that is determined in an alternativefashion, such as mass spectrometry.

There are specific examples of using algorithmic elements to improvebreakpoint based AST calling. One example is the use of resistancemechanism detection to adjust phenotype result calling. Each resistancemechanism can have one or more antibiotic substrates associated with itsactivity which are known a priori. These mechanisms can also havedifferent time-frames in which their activity can be detected. Some ofthese resistance mechanisms do not have robust activity within 4 hoursand can only be detected phenotypically after much longer incubationtimes (12-24 hours). For these resistance mechanisms an organism may beidentified as susceptible to a given drug simply because the resistancemechanism has not manifested sufficiently within a 4 hour time frame.Detection of these types of resistance mechanisms via separate PCR wellsallows for the correction of discordant phenotypic results. A specificexample is Serratia marcescens that sometimes encodes a SMEcarbapenemase resistance mechanism which is inducible, but not within a4 hour time frame. Thus these resistant S. marcescens strains willappear to be phenotypically susceptible to meropenem, but detection ofthe SME gene will allow the correct phenotypic prediction which ismeropenem resistance. Another example is the use of phenotypicsusceptibility from one or more antibiotics to predict susceptibilityfor other antibiotics. Because resistance mechanisms often haveoverlapping substrate specificity this means that susceptibility to someantibiotics is directly correlated with susceptibility to otherantibiotics. Likewise, resistance to some antibiotics is directlycorrelated with resistance to other antibiotics. This is similar to theExpert Rules system that many AST product manufacturers employ whereasdata collected from the PCR ID-AST assays of the present invention wouldbe employed as an adjunct to other methods of phenotypic resultinterpretation. A specific example would be a strain that is susceptibleto the antibiotic ertapenem will always be susceptible to the antibioticmeropenem due to the nature of carbapenemases and their substratespecificity which is always higher for degradation of ertapenem.Similarly, any strain that is resistant to meropenem will also beresistant to ertapenem for the same reason.

While the foregoing invention has been described in some detail forpurposes of clarity and understanding, it will be clear to one skilledin the art from a reading of this disclosure that various changes inform and detail can be made without departing from the true scope of theinvention. For example, all the techniques and apparatus described abovecan be used in various combinations. All publications, patents, patentapplications, and/or other documents cited in this application areincorporated by reference in their entirety for all purposes to the sameextent as if each individual publication, patent, patent application,and/or other document were individually indicated to be incorporated byreference for all purposes.

1. A method to simultaneously identify and determine the antimicrobialsusceptibility for one or more antimicrobial(s) of two or more differentmicroorganisms in a biological sample comprising: a) obtaining thebiological sample in which the two or more different microorganisms arebelieved to be present; b) optionally culturing the biological sampleunder conditions that facilitate growth of the two or more differentmicroorganisms and optionally normalizing the cultured biological samplesuch that the two or more different microorganisms reach a desiredconcentration; c) adding the biological sample in two or more reactionwells, whereby the one or more antimicrobial(s) is absent in at leastone reaction well, and whereby the one or more antimicrobial(s) ispresent in one or more reaction wells at one concentration or at morethan one varying concentrations, wherein in at least one reaction well,the concentration of the one or more antimicrobial(s) is either theMinimum Inhibitory Concentration (MIC) or the concentration used toclassify the two or more different microorganisms as Sensitive,Intermediate or Resistant to the one or more antimicrobial(s); d)incubating the biological sample in the presence or absence of the oneor more antimicrobial(s) for a period of time required to detectinhibition of growth; e) performing a quantitative real-time PCR assayin each of the two or more reaction wells, whereby, each PCR assaycomprises: (i) an amplifying step with at least a first set of primersand a second set of primers, wherein the first set of primersselectively anneals to a first target gene in a first microorganism andproduces a first amplification product if the first microorganism ispresent in the biological sample, and wherein the second set of primersselectively anneals to a second target gene in a second microorganismand produces a second amplification product if the second microorganismis present in the biological sample, and (ii) a hybridizing step whereina first detectable probe selectively anneals to the first amplificationproduct and generates a first signal and a second detectable probelabeled with a second fluorescent dye selectively anneals to the secondamplification product and generates a second signal that isdistinguishable from the first signal; f) identifying the two or moredifferent microorganisms whereby detection of the first signal isindicative of the presence of the first microorganism and detection ofthe second signal is indicative of the presence of the secondmicroorganism; and g) determining the antimicrobial susceptibility ofthe two or more different microorganisms by comparing the first andsecond_signals detected in the at least one reaction well where the oneor more antimicrobial(s) is absent to the first and second signalsdetected in the one or more reaction well(s) where the one or moreantimicrobial(s) is present; wherein steps e), f), and g), are allperformed simultaneously in each of the two or more reaction wells. 2.The method of claim 1 wherein the first and second target genes areselected from the group consisting of rplP, ompA, tuf, rpoB, ddl, ddlA,fdnG, sodA, gyrB, O-antigen acetylase, ecfX, tusA, CPE, sip, and nuc. 3.The method of claim 1 wherein the first microorganism is bacteria in thetaxonomic Order Enterobacterales.
 4. The method of claim 3 wherein thefirst target gene is selected from rplP, gyrB, and rpoB.
 5. The methodof claim 1 wherein the first microorganism is Pseudomonas aeruginosa. 6.The method of claim 5 wherein the first target gene is selected fromtuf, gyrB, 0-antigen acetylase and rpoB.
 7. The method of claim 1wherein the first microorganism is Acinetobacter baumannii.
 8. Themethod of claim 7 wherein the first target gene is selected from ompA,rpoB, and gyrB.
 9. The method of claim 1 wherein the first microorganismis bacteria in the taxonomic Genus Enterococcus.
 10. The method of claim9 wherein the first target gene is selected from rpoB, ddl, and gyrB.11. The method of claim 1 wherein the first microorganism isStaphylococcus aureus.
 12. The method of claim 11 wherein the firsttarget gene is selected from tuf, ddlA, and gyrB.
 13. The method ofclaim 1 wherein the first microorganism is bacteria in the taxonomicGenus Streptococcus.
 14. The method of claim 13 wherein the first targetgene is selected from tuf, sip, gyrB and ddlA.
 15. The method of claim 1wherein the first microorganism is fungus in the taxonomic GenusCandida.
 16. The method of claim 15 wherein the first target gene isselected from 18s rRNA and 5.8s rRNA.
 17. The method of claim 1 whereindetermining the antimicrobial susceptibility of the two or moredifferent microorganisms further comprises using one or moremathematical relationships from data derived from the PCR assay.
 18. Themethod of claim 18 wherein the mathematical relationship is selectedfrom Threshold Cycle (Ct), Slope, Inflection of a sigmoid curve fit,Absolute Fluorescence Intensity (AFI), or Endpoint Relative Intensity(ERI), or a combination thereof.
 19. The method of claim 18 wherein themathematical relationship is a relative expression between differentantimicrobial concentrations or between different antimicrobials and isselected from ΔCt, 2{circumflex over ( )}(ΔCt), ΔInflection, ΔΔFI, orΔERI, or a combination thereof.